Research workbench
Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. northeast structural genomics consortium target id DR64A
Analyse Crystal structure of a domain of ribosome-associated factor Y from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LYV
- Type
- protein
- Length
- 321 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-associated factor Y
- UniProt
- Q5XAQ7
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-associated factor Y | protein | 60 | 15% helix, 33% strand | Q5XAQ7 |
| B, C | Ribosome-associated factor Y | protein | 58 | 17% helix, 34% strand | Q5XAQ7 |
| D | Ribosome-associated factor Y | protein | 46 | 24% helix, 39% strand | Q5XAQ7 |
| E | Ribosome-associated factor Y | protein | 50 | 22% helix, 32% strand | Q5XAQ7 |
| F | Ribosome-associated factor Y | protein | 49 | 18% helix, 33% strand | Q5XAQ7 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.77 | 0.82 | 53 | empty |
| 2 | 238 | 0.54 | 0.77 | 34 | empty |
| 3 | 275 | 0.53 | 0.75 | 29 | empty |
| 4 | 145 | 0.51 | 0.79 | 16 | empty |
| 5 | 148 | 0.51 | 0.79 | 19 | empty |
Interfaces
10 interfaces between chains.
- C–F · 1288 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 904 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 381 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 261 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3LYV · Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes… · the same entry in another collection · chain F against F, TM-score 1.00
- Q5XAQ7 · AlphaFold monomer V2.0 prediction for ribosome hibernation promotion factor (Q5XAQ7) · a predicted model of the same protein · chain D against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5XAQ7
- Elsewhere: RCSB PDB 3LYV · PDBe 3LYV · UniProt Q5XAQ7
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