MolNFT v1 · #139070 · protein
Vapbc from mycobacterium tuberculosis
5X3T · Antitoxin VAPB26: “Vapbc from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.68). MolNFT v1 #139070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X3T
- Type
- protein
- Length
- 810 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin VAPB26; Ribonuclease VAPC26
- EC
- 3.1.-.-
- UniProt
- O53778, O53779
- Ligands
- MG
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antitoxin VAPB26 | protein | 70 | 44% helix, 9% strand | O53778 |
| E, G | Antitoxin VAPB26 | protein | 61 | 41% helix, 5% strand | O53778 |
| B, D, F, H | Ribonuclease VAPC26 (EC 3.1.-.-) | protein | 137 | 55% helix, 11% strand | O53779 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.68 | 0.80 | 50 | empty |
| 2 | 435 | 0.66 | 0.78 | 52 | empty |
| 3 | 213 | 0.63 | 0.83 | 36 | MG |
| 4 | 179 | 0.61 | 0.83 | 29 | empty |
| 5 | 164 | 0.59 | 0.82 | 27 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1449 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1441 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1322 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1321 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1225 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5X3T · VapBC from Mycobacterium tuberculosis · the same entry in another collection · chain H against H, TM-score 1.00
- O53779 · AlphaFold monomer V2.0 prediction for ribonuclease VAPC26 (O53779) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O53778 · AlphaFold monomer V2.0 prediction for antitoxin VAPB26 (O53778) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 O53778
- Every structure of UniProt O53779
- Elsewhere: RCSB PDB 5X3T · PDBe 5X3T · UniProt O53778 · UniProt O53779
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