Equivalence class DNA_2.0_96364.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3FL6|1|A+ 3FL6|1|B (rep) | 5'-D(*CP*GP*CP*AP*CP*GP*C)-3', 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3' | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-ray diffraction | 1.17 | 14 | 2009-12-29 | ||||
| 2 | 3FL6|1|C+ 3FL6|1|D | 5'-D(*CP*GP*CP*AP*CP*GP*C)-3', 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3' | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-ray diffraction | 1.17 | 14 | 2009-12-29 | ||||
| 3 | 1M6R|1|A+ 1M6R|1|B | 5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3' | Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang | X-ray diffraction | 1.54 | 12 | 2003-02-25 | ||||
| 4 | 3EYI|1|C+ 3EYI|1|D | 5'-TCGCGCG-3' | The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA | X-ray diffraction | 1.45 | 13 | 2009-01-13 | ||||
| 5 | 1MF5|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT Quadruplex | X-ray diffraction | 1.1 | 7 | 2003-02-11 | ||||
| 6 | 1MF5|1|B | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT Quadruplex | X-ray diffraction | 1.1 | 7 | 2003-02-11 | ||||
| 7 | 1UB8|1|A+ 1UB8|1|B | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 14 | 2004-03-09 | ||||
| 8 | 1UB8|1|C+ 1UB8|1|D | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 14 | 2004-03-09 | ||||
| 9 | 1UB8|1|E+ 1UB8|1|F | 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-ray diffraction | 1.6 | 14 | 2004-03-09 | ||||
| 10 | 2Z70|1|B | DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DTP*DCP*DGP*DCP*DG)-3') | E.coli RNase 1 in complex with d(CGCGATCGCG) | X-ray diffraction | 1.7 | 4 | 2008-06-24 | ||||
| 11 | 2AXY|1|E | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 7 | 2005-09-27 | ||||
| 12 | 2AXY|1|F | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 5 | 2005-09-27 | ||||
| 13 | 2AXY|1|G | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 6 | 2005-09-27 | ||||
| 14 | 2AXY|1|H | C-rich strand of human telomeric dna | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-ray diffraction | 1.7 | 5 | 2005-09-27 | ||||
| 15 | 2PY5|1|D | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 6 | 2007-07-17 | ||||
| 16 | 2PY5|1|E | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 6 | 2007-07-17 | ||||
| 17 | 2PY5|1|J | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 6 | 2007-07-17 | ||||
| 18 | 2PY5|1|L | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 4 | 2007-07-17 | ||||
| 19 | 2PY5|1|Y | 5'-d(GGACTTT)-3' | Phi29 DNA polymerase complexed with single-stranded DNA | X-ray diffraction | 1.6 | 6 | 2007-07-17 | ||||
| 20 | 2P2R|1|B | C-rich strand of human telomeric DNA | Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA | X-ray diffraction | 1.6 | 7 | 2007-06-12 | ||||
| 21 | 2WBS|1|F+ 2WBS|1|G | 5'-D(*GP*AP*GP*GP*CP*GP*CP)-3', 5'-D(*GP*CP*GP*CP*CP*TP*CP)-3' | Mus musculus | Crystal structure of the zinc finger domain of Klf4 bound to its target DNA | X-ray diffraction | 1.7 | 14 | 2010-04-07 | |||
| 22 | 1SFU|1|C+ 1SFU|1|D | 5'-D(*T*CP*GP*CP*GP*CP*G)-3' | Crystal structure of the viral Zalpha domain bound to left-handed Z-DNA | X-ray diffraction | 2 | 12 | 2004-08-17 | ||||
| 23 | 2HEO|1|B+ 2HEO|1|E | 5'-D(*TP*CP*GP*CP*GP*CP*G)-3' | General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers. | X-ray diffraction | 1.7 | 12 | 2006-11-21 | ||||
| 24 | 1J75|1|B | 5'-D(*TP*CP*GP*CP*GP*CP*G)-3' | Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA | X-ray diffraction | 1.85 | 7 | 2001-09-01 | ||||
| 25 | 1QYL|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Vanadium | X-ray diffraction | 1 | 7 | 2003-10-21 | ||||
| 26 | 1QYK|1|A | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Barium | X-ray diffraction | 1.4 | 7 | 2003-10-21 | ||||
| 27 | 1QYK|1|B | 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' | GCATGCT + Barium | X-ray diffraction | 1.4 | 7 | 2003-10-21 | ||||
| 28 | 1FIU|1|I+ 1FIU|1|J | DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3') | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-ray diffraction | 1.6 | 0 | 2001-02-07 | ||||
| 29 | 1FIU|1|K+ 1FIU|1|L | DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3') | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-ray diffraction | 1.6 | 0 | 2001-02-07 | ||||
| 30 | 331D|1|A+ 331D|1|B | DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3') | CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S | X-ray diffraction | 1.65 | 14 | 1997-09-24 | ||||
| 31 | 313D|1|A+ 313D|1|B | DNA (5'-D(*GP*(5CM)P*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR | X-ray diffraction | 1.68 | 14 | 1997-08-05 | ||||
| 32 | 1PUP|1|A | PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2) | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-ray diffraction | 1.7 | 0 | 1997-02-25 | ||||
| 33 | 1PUP|1|B | PNA (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-NH2) | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-ray diffraction | 1.7 | 0 | 1997-02-25 | ||||
| 34 | 184D|1|A | DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3') | SELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRUCTURE OF D(GCATGCT) AT 1.8 ANGSTROMS RESOLUTION | X-ray diffraction | 1.8 | 7 | 1995-07-10 | ||||
| 35 | 312D|1|A+ 312D|1|B | DNA (5'-D(*CP*CP*GP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR | X-ray diffraction | 1.8 | 14 | 1997-08-28 | ||||
| 36 | 314D|1|A+ 314D|1|B | DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3'), DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3') | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR | X-ray diffraction | 1.9 | 14 | 1997-08-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | 1MF5|1|B | GCATGCT Quadruplex | X-RAY DIFFRACTION | 1.1 | 7 | quadruplex,structure | ||
| 2 | 1QYK|1|A | GCATGCT + Barium | X-RAY DIFFRACTION | 1.4 | 7 | quadruplex,structure | ||
| 3 | 184D|1|A | SELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRUCTURE OF D(GCATGCT) AT 1.8 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.8 | 7 | quadruplex,structure | ||
| 4 | 1QYL|1|A | GCATGCT + Vanadium | X-RAY DIFFRACTION | 1 | 7 | quadruplex,structure | ||
| 5 | 1MF5|1|A | GCATGCT Quadruplex | X-RAY DIFFRACTION | 1.1 | 7 | quadruplex,structure | ||
| 6 | 1QYK|1|B | GCATGCT + Barium | X-RAY DIFFRACTION | 1.4 | 7 | quadruplex,structure | ||
| 7 | 2PY5|1|D | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 6 | enzyme,polymerase,transferase | ||
| 8 | 2PY5|1|E | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 6 | enzyme,polymerase,transferase | ||
| 9 | 2AXY|1|E | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 7 | post-transcriptional,regulatory | ||
| 10 | 2AXY|1|H | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 5 | post-transcriptional,regulatory | ||
| 11 | 2AXY|1|F | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 5 | post-transcriptional,regulatory | ||
| 12 | 2AXY|1|G | Crystal Structure of KH1 domain of human Poly(C)-binding protein-2 with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.7 | 6 | post-transcriptional,regulatory | ||
| 13 | 1UB8|1|E+ 1UB8|1|F | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 14 | double helix,feature,mispair,structure | ||
| 14 | 1UB8|1|A+ 1UB8|1|B | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 14 | double helix,feature,mispair,structure | ||
| 15 | 1UB8|1|C+ 1UB8|1|D | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | X-RAY DIFFRACTION | 1.6 | 14 | double helix,feature,mispair,structure | ||
| 16 | 2WBS|1|F+ 2WBS|1|G | Crystal structure of the zinc finger domain of Klf4 bound to its target DNA | X-RAY DIFFRACTION | 1.7 | 14 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 17 | 1FIU|1|K+ 1FIU|1|L | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-RAY DIFFRACTION | 1.6 | 0 | enzyme,hydrolase,nuclease | ||
| 18 | 1FIU|1|I+ 1FIU|1|J | TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA | X-RAY DIFFRACTION | 1.6 | 0 | enzyme,hydrolase,nuclease | ||
| 19 | 2PY5|1|L | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 4 | enzyme,polymerase,transferase | ||
| 20 | 3FL6|1|C+ 3FL6|1|D | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-RAY DIFFRACTION | 1.17 | 14 | B-form double helix,double helix,structure | ||
| 21 | 2PY5|1|J | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 6 | enzyme,polymerase,transferase | ||
| 22 | 2PY5|1|Y | Phi29 DNA polymerase complexed with single-stranded DNA | X-RAY DIFFRACTION | 1.6 | 6 | enzyme,polymerase,transferase | ||
| 23 | 2P2R|1|B | Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA | X-RAY DIFFRACTION | 1.6 | 7 | post-transcriptional,regulatory | ||
| 24 | 314D|1|A+ 314D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR | X-RAY DIFFRACTION | 1.9 | 14 | Z-form double helix,double helix,structure | ||
| 25 | 331D|1|A+ 331D|1|B | CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S | X-RAY DIFFRACTION | 1.65 | 14 | Z-form double helix,double helix,structure | ||
| 26 | 312D|1|A+ 312D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR | X-RAY DIFFRACTION | 1.8 | 14 | Z-form double helix,double helix,structure | ||
| 27 | 313D|1|A+ 313D|1|B | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR | X-RAY DIFFRACTION | 1.68 | 14 | Z-form double helix,double helix,structure | ||
| 28 | 3EYI|1|C+ 3EYI|1|D | The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA | X-RAY DIFFRACTION | 1.45 | 13 | Z-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 29 | 1M6R|1|A+ 1M6R|1|B | Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang | X-RAY DIFFRACTION | 1.54 | 12 | Z-form double helix,double helix,structure | ||
| 30 | 1SFU|1|C+ 1SFU|1|D | Crystal structure of the viral Zalpha domain bound to left-handed Z-DNA | X-RAY DIFFRACTION | 2 | 12 | Z-form double helix,double helix,structure | enzyme,hydrolase | |
| 31 | 2HEO|1|B+ 2HEO|1|E | General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers. | X-RAY DIFFRACTION | 1.7 | 12 | Z-form double helix,double helix,structure | cell cycle,regulatory | |
| 32 | 1J75|1|B | Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA | X-RAY DIFFRACTION | 1.85 | 7 | Z-form double helix,double helix,structure | cell cycle,regulatory | |
| 33 | 3FL6|1|A+ 3FL6|1|B | Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC) | X-RAY DIFFRACTION | 1.17 | 14 | B-form double helix,double helix,structure | ||
| 34 | 1PUP|1|B | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.7 | 0 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 35 | 1PUP|1|A | CRYSTAL STRUCTURE OF A PEPTIDE NUCLEIC ACID (PNA) DUPLEX AT 1.7 ANGSTROMS RESOLUTION | X-RAY DIFFRACTION | 1.7 | 0 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 36 | 2Z70|1|B | E.coli RNase 1 in complex with d(CGCGATCGCG) | X-RAY DIFFRACTION | 1.7 | 4 | enzyme,hydrolase,nuclease |
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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