Research workbench
Crystal structure of addiction module from mycobacterial species
Analyse Crystal structure of addiction module from mycobacterial species in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XGR
- Type
- protein
- Length
- 623 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease VAPC30; Antitoxin VAPB30
- EC
- 3.1.-.-
- UniProt
- P9WF77, P9WJ35
- Ligands
- MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, E | Ribonuclease VAPC30 (EC 3.1.-.-) | protein | 128 | 56% helix, 13% strand | P9WF77 |
| C | Ribonuclease VAPC30 (EC 3.1.-.-) | protein | 126 | 56% helix, 11% strand | P9WF77 |
| B | Antitoxin VAPB30 | protein | 33 | 39% helix, 0% strand | P9WJ35 |
| H | Antitoxin VAPB30 | protein | 24 | 42% helix, 0% strand | P9WJ35 |
| F | Antitoxin VAPB30 | protein | 24 | 46% helix, 0% strand | P9WJ35 |
| D | Antitoxin VAPB30 | protein | 32 | 50% helix, 0% strand | P9WJ35 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.68 | 0.75 | 74 | empty |
| 2 | 205 | 0.56 | 0.80 | 30 | empty |
| 3 | 238 | 0.56 | 0.78 | 29 | empty |
| 4 | 200 | 0.52 | 0.77 | 28 | MG |
| 5 | 195 | 0.49 | 0.76 | 26 | empty |
Interfaces
15 interfaces between chains.
- G–E · 1179 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1169 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1144 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1085 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 931 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4XGR · Crystal structure of addiction module from Mycobacterial species · the same entry in another collection · chain D against D, TM-score 1.00
- P9WF77 · AlphaFold monomer V2.0 prediction for ribonuclease VAPC30 (P9WF77) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P9WJ35 · AlphaFold monomer V2.0 prediction for antitoxin VAPB30 (P9WJ35) · a predicted model of the same protein · chain D against A, TM-score 0.71
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 P9WF77
- Every structure of UniProt P9WJ35
- Elsewhere: RCSB PDB 4XGR · PDBe 4XGR · UniProt P9WF77 · UniProt P9WJ35
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