Research workbench
Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2d (OA-2d)
Analyse Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2d (OA-2d) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYM
- Type
- protein
- Length
- 9,000 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Helicobacter pylori
- Molecule
- Vacuolating cytotoxin autotransporter
- UniProt
- Q48245
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · resolution 3.6 · 1 distinct chain · 5% helix, 32% 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, 32% 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 | 964 | 0.74 | 0.77 | 89 | empty |
| 2 | 987 | 0.73 | 0.77 | 96 | empty |
| 3 | 979 | 0.73 | 0.77 | 102 | empty |
| 4 | 1044 | 0.73 | 0.77 | 107 | empty |
| 5 | 929 | 0.73 | 0.77 | 95 | empty |
Interfaces
23 interfaces between chains.
- D–E · 1086 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1084 Ų buried · 17 hydrogen bonds · protein-protein
- G–L · 1083 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1079 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1076 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6NYM · Helicobacter pylori vacuolating cytotoxin a oligomeric assembly 2D (oa-2D) · 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 6NYM · PDBe 6NYM · UniProt Q48245
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