Research workbench
Crystal structure of hexameric complex of SA2YOEB-SA2YEFM toxin- antitoxin from staphylococcus aureus
Analyse Crystal structure of hexameric complex of SA2YOEB-SA2YEFM toxin- antitoxin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V5Y
- Type
- protein
- Length
- 456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin; Putative mRNA interferase yoeb
- UniProt
- Q2FVF7, Q2FVF8
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Antitoxin | protein | 85 | 59% helix, 16% strand | Q2FVF7 |
| A, C | Antitoxin | protein | 56 | 55% helix, 18% strand | Q2FVF7 |
| E, F | Putative mRNA interferase yoeb | protein | 87 | 32% helix, 29% strand | Q2FVF8 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.85 | 0.95 | 38 | empty |
| 2 | 300 | 0.53 | 0.75 | 36 | empty |
| 3 | 216 | 0.52 | 0.77 | 26 | empty |
| 4 | 248 | 0.50 | 0.75 | 42 | empty |
| 5 | 143 | 0.46 | 0.77 | 23 | empty |
Interfaces
15 interfaces between chains.
- B–E · 1635 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1582 Ų buried · 37 hydrogen bonds · protein-protein
- D–C · 1457 Ų buried · 28 hydrogen bonds · protein-protein
- B–A · 1451 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 407 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7V5Y · Crystal structure of hexameric complex of Sa2YoeB-Sa2YefM toxin-antitoxin from… · the same entry in another collection · chain B against B, TM-score 1.00
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 Q2FVF7
- Every structure of UniProt Q2FVF8
- Elsewhere: RCSB PDB 7V5Y · PDBe 7V5Y · UniProt Q2FVF7 · UniProt Q2FVF8
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