Equivalence class DNA_3.0_40131.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2AOR|1|C+ 2AOR|1|D (rep) | 5'-D(*CP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*AP*TP*CP*CP*TP*G)-3' | Crystal structure of MutH-hemimethylated DNA complex | X-ray diffraction | 2 | 44 | 2005-10-11 | ||||
| 2 | 2HT0|1|D+ 2HT0|1|F+ 2HT0|1|E+ 2HT0|1|C | 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3', 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3', 5'-D(*TP*GP*AP*TP*AP*AP*GP*CP*AP*AP*TP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*C)-3' | IHF bound to doubly nicked DNA | X-ray diffraction | 2 | 70 | 2006-11-28 | ||||
| 3 | 3MVA|1|D+ 3MVA|1|E | 5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3'), 5'-D(*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3') | Crystal structure of human MTERF1 bound to the termination sequence | X-ray diffraction | 2.2 | 44 | 2010-06-30 | ||||
| 4 | 3MLN|1|C+ 3MLN|1|D | DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3') | synthetic construct | DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) | X-ray diffraction | 2.4 | 44 | 2010-12-01 | |||
| 5 | 3M9E|1|G+ 3M9E|1|H | DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3') | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-ray diffraction | 2.406 | 44 | 2010-08-18 | ||||
| 6 | 3M9E|1|C+ 3M9E|1|D | DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3') | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-ray diffraction | 2.406 | 44 | 2010-08-18 | ||||
| 7 | 2I13|1|E+ 2I13|1|F | 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3', 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3' | Aart, a six finger zinc finger designed to recognize ANN triplets | X-ray diffraction | 1.96 | 44 | 2006-10-03 | ||||
| 8 | 2I13|1|C+ 2I13|1|D | 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3', 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3' | Aart, a six finger zinc finger designed to recognize ANN triplets | X-ray diffraction | 1.96 | 44 | 2006-10-03 | ||||
| 9 | 1P47|1|C+ 1P47|1|D | 5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3', 5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3' | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-ray diffraction | 2.2 | 44 | 2003-06-24 | ||||
| 10 | 3IKT|1|C+ 3IKT|1|D | Rex operator DNA | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | X-ray diffraction | 2.26 | 44 | 2010-06-09 | ||||
| 11 | 2B9S|1|E+ 2B9S|1|D+ 2B9S|1|C | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3', 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | X-ray diffraction | 2.27 | 44 | 2006-01-17 | ||||
| 12 | 3MLP|1|G+ 3MLP|1|H | DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3') | synthetic construct | Early B-cell Factor 1 (Ebf1) bound to DNA | X-ray diffraction | 2.8 | 44 | 2010-12-01 | |||
| 13 | 3MLP|1|C+ 3MLP|1|D | DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3') | synthetic construct | Early B-cell Factor 1 (Ebf1) bound to DNA | X-ray diffraction | 2.8 | 44 | 2010-12-01 | |||
| 14 | 3MVB|1|D+ 3MVB|1|E | 5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3', 5'-D(*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3' | Crystal structure of a triple RFY mutant of human MTERF1 bound to the termination sequence | X-ray diffraction | 2.786 | 44 | 2010-06-30 | ||||
| 15 | 3FMT|1|G+ 3FMT|1|H | 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3' | Crystal structure of SeqA bound to DNA | X-ray diffraction | 2.983 | 43 | 2009-04-28 | ||||
| 16 | 3FMT|1|C+ 3FMT|1|D | 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3' | Crystal structure of SeqA bound to DNA | X-ray diffraction | 2.983 | 43 | 2009-04-28 | ||||
| 17 | 3IL2|1|C+ 3IL2|1|D | Rex operator DNA | Crystal structure of a Rex-family repressor R90D mutant/DNA complex from Thermus aquaticus | X-ray diffraction | 2.49 | 44 | 2010-06-09 | ||||
| 18 | 3JSO|1|C+ 3JSO|1|D | DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*GP*TP*A)-3') | Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex | X-ray diffraction | 2.29 | 44 | 2010-08-18 | ||||
| 19 | 3L2P|1|D+ 3L2P|1|B+ 3L2P|1|C | 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3', 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3', 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' | Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States | X-ray diffraction | 3 | 42 | 2010-07-14 | ||||
| 20 | 3F2C|1|T+ 3F2C|1|P | 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3', 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3' | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP and Mn | X-ray diffraction | 2.5 | 31 | 2009-01-20 | ||||
| 21 | 3MX4|1|I+ 3MX4|1|J | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 22 | 3MX4|1|M+ 3MX4|1|N | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 23 | 3MX4|1|O+ 3MX4|1|P | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 24 | 3JSP|1|C+ 3JSP|1|D | DNA (5'-D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*GP*CP*GP*CP*AP*TP*AP*CP*AP*GP*TP*A)-3') | Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex | X-ray diffraction | 2.9 | 44 | 2010-08-18 | ||||
| 25 | 3MX4|1|K+ 3MX4|1|L | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-ray diffraction | 2.5 | 44 | 2010-09-08 | ||||
| 26 | 3F2B|1|T+ 3F2B|1|P | 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3', 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3' | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn | X-ray diffraction | 2.39 | 31 | 2009-01-20 | ||||
| 27 | 3C25|1|C+ 3C25|1|D | DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3'), DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3') | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | X-ray diffraction | 2.5 | 44 | 2008-02-12 | ||||
| 28 | 2PI4|1|T+ 2PI4|1|P | 5'-D(*CP*TP*TP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3', 5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3' | T7RNAP complexed with a phi10 protein and initiating GTPs. | X-ray diffraction | 2.5 | 36 | 2007-06-19 | ||||
| 29 | 3NIC|1|K+ 3NIC|1|L | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-ray diffraction | 2.8 | 44 | 2010-09-08 | ||||
| 30 | 3NIC|1|I+ 3NIC|1|J | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-ray diffraction | 2.8 | 44 | 2010-09-08 | ||||
| 31 | 3NIC|1|M+ 3NIC|1|N | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-ray diffraction | 2.8 | 44 | 2010-09-08 | ||||
| 32 | 3NIC|1|O+ 3NIC|1|P | DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3') | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-ray diffraction | 2.8 | 44 | 2010-09-08 | ||||
| 33 | 2PI5|1|T+ 2PI5|1|P | 5'-D(*CP*TP*TP*C*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3', 5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3' | T7 RNA polymerase complexed with a phi10 promoter | X-ray diffraction | 2.9 | 32 | 2007-06-19 | ||||
| 34 | 3F2D|1|T+ 3F2D|1|P | 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3', 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3' | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn | X-ray diffraction | 2.51 | 31 | 2009-01-20 | ||||
| 35 | 2A0I|1|B | F plasmid single-stranded oriT DNA | F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA | X-ray diffraction | 2.72 | 10 | 2005-10-25 | ||||
| 36 | 1K4T|1|D+ 1K4T|1|C+ 1K4T|1|B | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-ray diffraction | 2.1 | 44 | 2002-12-04 | ||||
| 37 | 1QLN|1|T+ 1QLN|1|N | DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3), DNA (5-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3) | Escherichia virus T7 | STRUCTURE OF A TRANSCRIBING T7 RNA POLYMERASE INITIATION COMPLEX | X-ray diffraction | 2.4 | 36 | 2000-02-04 | |||
| 38 | 1A31|1|C+ 1A31|1|D | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*5IUP*5IU*TP*GP*AP*AP*AP*AP*AP*5IUP*5IUP*5IUP*5IUP*T)-3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*5IUP*5IUP*5IUP*5IUP*CP*AP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3') | HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-ray diffraction | 2.1 | 44 | 1998-08-28 | ||||
| 39 | 1RRJ|1|B+ 1RRJ|1|C | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T*GP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I | X-ray diffraction | 2.3 | 44 | 2004-07-06 | ||||
| 40 | 1PAR|1|E+ 1PAR|1|F | DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*T P*AP*CP*TP*AP*T)- 3'), DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*T P*AP*TP*CP*AP*T)- 3') | DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE | X-ray diffraction | 2.6 | 44 | 1994-07-31 | ||||
| 41 | 1REP|1|A+ 1REP|1|B | DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3'), DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3') | CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA | X-ray diffraction | 2.6 | 42 | 2000-02-09 | ||||
| 42 | 1HF0|1|M+ 1HF0|1|N | DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3', DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3' | Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer | X-ray diffraction | 2.7 | 44 | 2001-11-10 | ||||
| 43 | 1A35|1|C+ 1A35|1|D | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*AP*(BRU)P*(BRU)P*TP*TP*T)-3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ UP*T)-3') | HUMAN TOPOISOMERASE I/DNA COMPLEX | X-ray diffraction | 2.5 | 44 | 1998-08-28 | ||||
| 44 | 1RR8|1|A+ 1RR8|1|B | 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T*GP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I | X-ray diffraction | 2.6 | 44 | 2004-07-06 | ||||
| 45 | 1BDT|1|E+ 1BDT|1|F | DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)-3') | WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX | X-ray diffraction | 2.5 | 44 | 1999-02-16 | ||||
| 46 | 1SC7|1|D+ 1SC7|1|C+ 1SC7|1|B | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex | X-ray diffraction | 3 | 44 | 2005-04-19 | ||||
| 47 | 1BDV|1|E+ 1BDV|1|F | DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)-3') | ARC FV10 COCRYSTAL | X-ray diffraction | 2.8 | 44 | 1999-01-06 | ||||
| 48 | 1SEU|1|D+ 1SEU|1|C+ 1SEU|1|B | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | Human DNA Topoisomerase I (70 Kda) In Complex With The Indolocarbazole SA315F and Covalent Complex With A 22 Base Pair DNA Duplex | X-ray diffraction | 3 | 44 | 2005-04-19 | ||||
| 49 | 1T8I|1|D+ 1T8I|1|C+ 1T8I|1|B | 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' | Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin and Covalent Complex With A 22 Base Pair DNA Duplex | X-ray diffraction | 3 | 44 | 2005-05-31 | ||||
| 50 | 1A36|1|B+ 1A36|1|C | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*A P*TP*TP*TP*TP*T)- 3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*C P*TP*TP*TP*TP*T)- 3') | TOPOISOMERASE I/DNA COMPLEX | X-ray diffraction | 2.8 | 44 | 1998-08-12 | ||||
| 51 | 2A6O|1|C | 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3' | Crystal Structure of the ISHp608 Transposase in Complex with Stem-loop DNA | X-ray diffraction | 2.6 | 22 | 2005-10-25 | ||||
| 52 | 2A6O|1|D | 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3' | Crystal Structure of the ISHp608 Transposase in Complex with Stem-loop DNA | X-ray diffraction | 2.6 | 22 | 2005-10-25 | ||||
| 53 | 1AN2|1|B | DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3') | Mus musculus | RECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN | X-ray diffraction | 2.9 | 22 | 1997-09-17 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 3FMT|1|G+ 3FMT|1|H | Crystal structure of SeqA bound to DNA | X-RAY DIFFRACTION | 2.983 | 43 | B-form double helix,double helix,structure | DNA replication/repair,regulatory | |
| 2 | 3FMT|1|C+ 3FMT|1|D | Crystal structure of SeqA bound to DNA | X-RAY DIFFRACTION | 2.983 | 43 | B-form double helix,double helix,structure | DNA replication/repair,regulatory | |
| 3 | 3JSP|1|C+ 3JSP|1|D | Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex | X-RAY DIFFRACTION | 2.9 | 44 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 4 | 3JSO|1|C+ 3JSO|1|D | Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex | X-RAY DIFFRACTION | 2.29 | 44 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 5 | 1BDV|1|E+ 1BDV|1|F | ARC FV10 COCRYSTAL | X-RAY DIFFRACTION | 2.8 | 44 | double helix,structure | DNA-binding transcription factor (TF),MetR homology,other α-helix,regulatory,transcription | |
| 6 | 1BDT|1|E+ 1BDT|1|F | WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MetR homology,other α-helix,regulatory,transcription | |
| 7 | 1PAR|1|E+ 1PAR|1|F | DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE | X-RAY DIFFRACTION | 2.6 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MetR homology,other α-helix,regulatory,transcription | |
| 8 | 1RR8|1|A+ 1RR8|1|B | Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I | X-RAY DIFFRACTION | 2.6 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 9 | 1RRJ|1|B+ 1RRJ|1|C | Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I | X-RAY DIFFRACTION | 2.3 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 10 | 1SEU|1|D+ 1SEU|1|C+ 1SEU|1|B | Human DNA Topoisomerase I (70 Kda) In Complex With The Indolocarbazole SA315F and Covalent Complex With A 22 Base Pair DNA Duplex | X-RAY DIFFRACTION | 3 | 44 | double helix,structure | enzyme,isomerase | |
| 11 | 1K4T|1|D+ 1K4T|1|C+ 1K4T|1|B | HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-RAY DIFFRACTION | 2.1 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 12 | 1T8I|1|D+ 1T8I|1|C+ 1T8I|1|B | Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin and Covalent Complex With A 22 Base Pair DNA Duplex | X-RAY DIFFRACTION | 3 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 13 | 1SC7|1|D+ 1SC7|1|C+ 1SC7|1|B | Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex | X-RAY DIFFRACTION | 3 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 14 | 3MX4|1|K+ 3MX4|1|L | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 15 | 3MX4|1|O+ 3MX4|1|P | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 16 | 3NIC|1|I+ 3NIC|1|J | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 17 | 3NIC|1|O+ 3NIC|1|P | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 18 | 3NIC|1|M+ 3NIC|1|N | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 19 | 3NIC|1|K+ 3NIC|1|L | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 20 | 3MX4|1|M+ 3MX4|1|N | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 21 | 3MX4|1|I+ 3MX4|1|J | DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 22 | 1HF0|1|M+ 1HF0|1|N | Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer | X-RAY DIFFRACTION | 2.7 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 23 | 2B9S|1|E+ 2B9S|1|D+ 2B9S|1|C | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | X-RAY DIFFRACTION | 2.27 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 24 | 3IKT|1|C+ 3IKT|1|D | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | X-RAY DIFFRACTION | 2.26 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 25 | 3IL2|1|C+ 3IL2|1|D | Crystal structure of a Rex-family repressor R90D mutant/DNA complex from Thermus aquaticus | X-RAY DIFFRACTION | 2.49 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 26 | 1A36|1|B+ 1A36|1|C | TOPOISOMERASE I/DNA COMPLEX | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 27 | 1A35|1|C+ 1A35|1|D | HUMAN TOPOISOMERASE I/DNA COMPLEX | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 28 | 1A31|1|C+ 1A31|1|D | HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | X-RAY DIFFRACTION | 2.1 | 44 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 29 | 1AN2|1|B | RECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN | X-RAY DIFFRACTION | 2.9 | 22 | double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription | |
| 30 | 3M9E|1|C+ 3M9E|1|D | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 31 | 3M9E|1|G+ 3M9E|1|H | Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE | X-RAY DIFFRACTION | 2.406 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 32 | 1REP|1|A+ 1REP|1|B | CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA | X-RAY DIFFRACTION | 2.6 | 42 | B-form double helix,double helix,structure | DNA replication/repair,regulatory | |
| 33 | 3MLP|1|C+ 3MLP|1|D | Early B-cell Factor 1 (Ebf1) bound to DNA | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 34 | 3MLP|1|G+ 3MLP|1|H | Early B-cell Factor 1 (Ebf1) bound to DNA | X-RAY DIFFRACTION | 2.8 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 35 | 3MLN|1|C+ 3MLN|1|D | DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II) | X-RAY DIFFRACTION | 2.4 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 36 | 1P47|1|C+ 1P47|1|D | Crystal Structure of tandem Zif268 molecules complexed to DNA | X-RAY DIFFRACTION | 2.2 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 37 | 2I13|1|E+ 2I13|1|F | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 38 | 2I13|1|C+ 2I13|1|D | Aart, a six finger zinc finger designed to recognize ANN triplets | X-RAY DIFFRACTION | 1.96 | 44 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 39 | 2AOR|1|C+ 2AOR|1|D | Crystal structure of MutH-hemimethylated DNA complex | X-RAY DIFFRACTION | 2 | 44 | B-form double helix,double helix,structure | DNA replication/repair,enzyme,hydrolase,nuclease,regulatory | |
| 40 | 3C25|1|C+ 3C25|1|D | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | X-RAY DIFFRACTION | 2.5 | 44 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 41 | 3L2P|1|D+ 3L2P|1|B+ 3L2P|1|C | Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States | X-RAY DIFFRACTION | 3 | 42 | double helix,structure | enzyme,ligase | |
| 42 | 3MVB|1|D+ 3MVB|1|E | Crystal structure of a triple RFY mutant of human MTERF1 bound to the termination sequence | X-RAY DIFFRACTION | 2.786 | 44 | RNA-binding transcription factor,regulatory,transcription | ||
| 43 | 3MVA|1|D+ 3MVA|1|E | Crystal structure of human MTERF1 bound to the termination sequence | X-RAY DIFFRACTION | 2.2 | 44 | RNA-binding transcription factor,regulatory,transcription | ||
| 44 | 2HT0|1|D+ 2HT0|1|F+ 2HT0|1|E+ 2HT0|1|C | IHF bound to doubly nicked DNA | X-RAY DIFFRACTION | 2 | 70 | β-sheet,DNA-binding transcription factor (TF),IHF-like,regulatory,transcription | ||
| 45 | 3F2B|1|T+ 3F2B|1|P | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn | X-RAY DIFFRACTION | 2.39 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 46 | 3F2C|1|T+ 3F2C|1|P | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP and Mn | X-RAY DIFFRACTION | 2.5 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 47 | 3F2D|1|T+ 3F2D|1|P | DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn | X-RAY DIFFRACTION | 2.51 | 31 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 48 | 2PI4|1|T+ 2PI4|1|P | T7RNAP complexed with a phi10 protein and initiating GTPs. | X-RAY DIFFRACTION | 2.5 | 36 | enzyme,polymerase,transferase | ||
| 49 | 2PI5|1|T+ 2PI5|1|P | T7 RNA polymerase complexed with a phi10 promoter | X-RAY DIFFRACTION | 2.9 | 32 | enzyme,polymerase,transferase | ||
| 50 | 2A0I|1|B | F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA | X-RAY DIFFRACTION | 2.72 | 10 | enzyme,hydrolase | ||
| 51 | 2A6O|1|C | Crystal Structure of the ISHp608 Transposase in Complex with Stem-loop DNA | X-RAY DIFFRACTION | 2.6 | 22 | enzyme,recombinase | ||
| 52 | 2A6O|1|D | Crystal Structure of the ISHp608 Transposase in Complex with Stem-loop DNA | X-RAY DIFFRACTION | 2.6 | 22 | enzyme,recombinase | ||
| 53 | 1QLN|1|T+ 1QLN|1|N | STRUCTURE OF A TRANSCRIBING T7 RNA POLYMERASE INITIATION COMPLEX | X-RAY DIFFRACTION | 2.4 | 36 | enzyme,polymerase,transferase |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
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