Research workbench
Crystal structure of mycobacterium tuberculosis VAPBC11 toxin- antitoxin complex
Analyse Crystal structure of mycobacterium tuberculosis VAPBC11 toxin- antitoxin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A7V
- Type
- protein
- Length
- 795 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease VAPC11; Antitoxin VAPB11
- EC
- 3.1.-.-
- UniProt
- P9WFA5, P9WLU3
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ribonuclease VAPC11 (EC 3.1.-.-) | protein | 135 | 60% helix, 11% strand | P9WFA5 |
| K, D, U, H | Antitoxin VAPB11 | protein | 62 | 55% helix, 8% strand | P9WLU3 |
| C | Ribonuclease VAPC11 (EC 3.1.-.-) | protein | 139 | 59% helix, 12% strand | P9WFA5 |
| G | Ribonuclease VAPC11 (EC 3.1.-.-) | protein | 138 | 59% helix, 12% strand | P9WFA5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C, D, U
- 1PE · Pentaethylene glycol · additive · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.74 | 0.80 | 54 | empty |
| 2 | 82 | 0.71 | 0.95 | 23 | empty |
| 3 | 573 | 0.71 | 0.80 | 62 | empty |
| 4 | 113 | 0.48 | 0.80 | 20 | empty |
| 5 | 188 | 0.47 | 0.76 | 23 | 1PE |
Interfaces
20 interfaces between chains.
- D–U · 1517 Ų buried · 28 hydrogen bonds · protein-protein
- K–H · 1485 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1441 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1348 Ų buried · 30 hydrogen bonds · protein-protein
- E–G · 1293 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6A7V · Crystal structure of Mycobacterium tuberculosis VapBC11 toxin-antitoxin complex · the same entry in another collection · chain H against H, TM-score 1.00
- P9WFA5 · AlphaFold monomer V2.0 prediction for ribonuclease VAPC11 (P9WFA5) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P9WLU3 · AlphaFold monomer V2.0 prediction for antitoxin VAPB11 (P9WLU3) · a predicted model of the same protein · chain K against A, TM-score 0.58
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 P9WFA5
- Every structure of UniProt P9WLU3
- Elsewhere: RCSB PDB 6A7V · PDBe 6A7V · UniProt P9WFA5 · UniProt P9WLU3
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