Research workbench
Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2A (oa-2A)
Analyse Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2A (oa-2A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYG
- 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 · 5% 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 | 5% helix, 29% strand | Q48245 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.70 | 0.78 | 68 | empty |
| 2 | 691 | 0.70 | 0.78 | 68 | empty |
| 3 | 662 | 0.70 | 0.77 | 60 | empty |
| 4 | 642 | 0.69 | 0.77 | 55 | empty |
| 5 | 661 | 0.69 | 0.77 | 64 | empty |
Interfaces
24 interfaces between chains.
- H–I · 1085 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1085 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 1079 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1079 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1077 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6NYG · Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2a (OA-2a) · 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 6NYG · PDBe 6NYG · UniProt Q48245
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