MolNFT v1 · #158579 · protein
Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 1 (oa- 1)
6NYF · Vacuolating cytotoxin autotransporter: “Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 1 (oa- 1)”. Electron microscopy, 20 pockets (best druggability 0.70). MolNFT v1 #158579 on GenesisL1: 3D structure, binding…
- PDB
- 6NYF
- Type
- protein
- Length
- 4,500 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolating cytotoxin autotransporter
- UniProt
- Q48245
- Pockets
- 20 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 4% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Vacuolating cytotoxin autotransporter | protein | 750 | 4% helix, 29% strand | Q48245 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.70 | 0.77 | 60 | empty |
| 2 | 652 | 0.69 | 0.77 | 62 | empty |
| 3 | 649 | 0.69 | 0.77 | 67 | empty |
| 4 | 642 | 0.69 | 0.77 | 63 | empty |
| 5 | 638 | 0.68 | 0.77 | 61 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1119 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1118 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1116 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1111 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1111 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6NYF · Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) · the same entry in another collection · chain F against F, TM-score 1.00
- Q48245 · AlphaFold monomer V2.0 prediction for vacuolating cytotoxin autotransporter (Q48245) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q48245
- Elsewhere: RCSB PDB 6NYF · PDBe 6NYF · UniProt Q48245
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