MolNFT v1 · #171983 · protein
Crystal structure of the H. influenzae vapxd toxin-antitoxin complex
6ZN8 · Endoribonuclease vapd: “Crystal structure of the H. influenzae vapxd toxin-antitoxin complex”. X-ray diffraction, 2 pockets (best druggability 0.76). MolNFT v1 #171983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZN8
- Type
- protein
- Length
- 489 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease vapd; Vapx
- EC
- 3.1.-.-
- UniProt
- Q4QN95, Q4QN94
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Endoribonuclease vapd (EC 3.1.-.-) | protein | 90 | 39% helix, 29% strand | Q4QN95 |
| B | Endoribonuclease vapd (EC 3.1.-.-) | protein | 91 | 40% helix, 24% strand | Q4QN95 |
| C | Vapx | protein | 66 | 11% helix, 39% strand | Q4QN94 |
| F | Vapx | protein | 62 | 13% helix, 42% strand | Q4QN94 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.76 | 0.79 | 105 | empty |
| 2 | 76 | 0.53 | 0.86 | 20 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1506 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1502 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 856 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 819 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 467 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 6ZN8 · Crystal structure of the H. influenzae VapXD toxin-antitoxin complex · the same entry in another collection · chain A against A, 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 Q4QN95
- Every structure of UniProt Q4QN94
- Elsewhere: RCSB PDB 6ZN8 · PDBe 6ZN8 · UniProt Q4QN95 · UniProt Q4QN94
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