Research workbench
Cryo-EM structure of helicobacter pylori vaca hexamer
Analyse Cryo-EM structure of helicobacter pylori vaca hexamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ODY
- Type
- protein
- Length
- 4,158 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolating cytotoxin autotransporter
- UniProt
- Q48245
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 4% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Vacuolating cytotoxin autotransporter | protein | 693 | 4% helix, 27% 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 | 1040 | 0.86 | 0.88 | 142 | empty |
| 2 | 1128 | 0.86 | 0.88 | 136 | empty |
| 3 | 1059 | 0.86 | 0.88 | 139 | empty |
| 4 | 987 | 0.86 | 0.87 | 136 | empty |
| 5 | 1149 | 0.86 | 0.87 | 136 | empty |
Interfaces
6 interfaces between chains.
- B–C · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 418 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 417 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 417 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6ODY · Cryo-EM structure of Helicobacter pylori VacA hexamer · the same entry in another collection · chain C against C, TM-score 1.00
- Q48245 · AlphaFold monomer V2.0 prediction for vacuolating cytotoxin autotransporter (Q48245) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 6ODY · PDBe 6ODY · UniProt Q48245
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