Research workbench
Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2E (oa-2E)
Analyse Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2E (oa-2E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYN
- 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 0.71
Structure
electron microscopy · 1 distinct chain · 4% helix, 29% 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, 29% 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 | 785 | 0.71 | 0.77 | 73 | empty |
| 2 | 644 | 0.69 | 0.78 | 60 | empty |
| 3 | 623 | 0.69 | 0.78 | 61 | empty |
| 4 | 641 | 0.69 | 0.77 | 61 | empty |
| 5 | 627 | 0.69 | 0.78 | 67 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1110 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 1110 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 1108 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1108 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1107 Ų buried · 11 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 6NYN · PDBe 6NYN · UniProt Q48245
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