Research workbench
Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2C (oa-2C)
Analyse Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2C (oa-2C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYL
- 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 0.73
Structure
electron microscopy · 1 distinct chain · 4% helix, 28% 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, 28% strand | Q48245 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.73 | 0.77 | 93 | empty |
| 2 | 882 | 0.73 | 0.77 | 89 | empty |
| 3 | 924 | 0.73 | 0.77 | 84 | empty |
| 4 | 900 | 0.72 | 0.77 | 89 | empty |
| 5 | 863 | 0.72 | 0.77 | 78 | empty |
Interfaces
24 interfaces between chains.
- K–L · 1137 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1126 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1122 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1122 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1120 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6NYL · Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2c (OA-2c) · the same entry in another collection · chain L against L, 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 Q48245
- Elsewhere: RCSB PDB 6NYL · PDBe 6NYL · UniProt Q48245
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