J4_5HD1_028
3D structure
- PDB id
- 5HD1 (explore in PDB, NAKB, or RNA 3D Hub)
- Description
- Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus thermophilus 70S ribosome
- Experimental method
- X-RAY DIFFRACTION
- Resolution
- 2.7 Å
Loop
- Sequence
- G(4SU)GG*CGUC*GAAGGUCG*CC
- Length
- 18 nucleotides
- Bulged bases
- 5HD1|1|2x|4SU|8, 5HD1|1|2x|U|47, 5HD1|1|2x|C|48
- QA status
- Modified nucleotides: 4SU
Sequence variability
-
If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.
- R3DSVS
Structural variability across Equivalence Class
-
The link below will give the loop's structural variability across the equivalence class for this chain.
- R3DMCS EC
Structural variability across Rfam
-
If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.
- R3DMCS Rfam
- J4_5HD1_028 not in the Motif Atlas
- Homologous match to J4_1QF6_001
- Geometric discrepancy: 0.286
- The information below is about J4_1QF6_001
- Detailed Annotation
- tRNA junction
- Broad Annotation
- No text annotation
- Motif group
- J4_94519.1
- Basepair signature
- cWW-F-F-F-F-F-cWW-F-F-F-F-cWW-cWW
- Number of instances in this motif group
- 2
Unit IDs
5HD1|1|2x|G|7
5HD1|1|2x|4SU|8
5HD1|1|2x|G|9
5HD1|1|2x|G|10
*
5HD1|1|2x|C|25
5HD1|1|2x|G|26
5HD1|1|2x|U|27
5HD1|1|2x|C|28
*
5HD1|1|2x|G|42
5HD1|1|2x|A|43
5HD1|1|2x|A|44
5HD1|1|2x|G|45
5HD1|1|2x|G|46
5HD1|1|2x|U|47
5HD1|1|2x|C|48
5HD1|1|2x|G|49
*
5HD1|1|2x|C|65
5HD1|1|2x|C|66
Current chains
- Chain 2x
- P-site tRNA
Nearby chains
- Chain 20
- 50S ribosomal protein L27
- Chain 2A
- Large subunit ribosomal RNA; LSU rRNA
- Chain 2Q
- 50S ribosomal protein L16
- Chain 2a
- Small subunit ribosomal RNA; SSU rRNA
- Chain 2m
- 30S ribosomal protein S13
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