Research workbench
Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2B (oa-2B)
Analyse Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2B (oa-2B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYJ
- Type
- protein
- Length
- 9,000 residues
- Chains
- 12
- 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, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Vacuolating cytotoxin autotransporter | protein | 750 | 4% helix, 30% strand | Q48245 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.70 | 0.77 | 67 | empty |
| 2 | 703 | 0.70 | 0.77 | 67 | empty |
| 3 | 653 | 0.69 | 0.77 | 65 | empty |
| 4 | 685 | 0.69 | 0.77 | 71 | empty |
| 5 | 649 | 0.69 | 0.77 | 58 | empty |
Interfaces
24 interfaces between chains.
- E–F · 1118 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- G–L · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1116 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 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 6NYJ · PDBe 6NYJ · UniProt Q48245
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