MolNFT v1 · #153825 · protein
Crystal structure of N-terminal domain of VAPB46 antitoxin from mycobacterium tuberculosis
6JQY · Antitoxin VAPB46: “Crystal structure of N-terminal domain of VAPB46 antitoxin from mycobacterium tuberculosis”. X-ray diffraction, 1 pocket (best druggability 0.29). MolNFT v1 #153825 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JQY
- Type
- protein
- Length
- 174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin VAPB46
- UniProt
- P9WF12
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antitoxin VAPB46 | protein | 44 | 34% helix, 39% strand | P9WF12 |
| B | Antitoxin VAPB46 | protein | 43 | 37% helix, 37% strand | P9WF12 |
| D | Antitoxin VAPB46 | protein | 43 | 35% helix, 37% strand | P9WF12 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.29 | 0.74 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 859 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 829 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 382 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JQY · Crystal structure of N-terminal domain of VapB46 antitoxin from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WF12 · AlphaFold monomer V2.0 prediction for antitoxin VAPB46 (P9WF12) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P9WF12
- Elsewhere: RCSB PDB 6JQY · PDBe 6JQY · UniProt P9WF12
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