Research workbench
Crystal structure of cags (HP0534, CAG13) from helicobacter pylori
Analyse Crystal structure of cags (HP0534, CAG13) from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G3V
- Type
- protein
- Length
- 672 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cag pathogenicity island protein 13; (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK)
- UniProt
- P97227
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cag pathogenicity island protein 13 | protein | 161 | 73% helix, 1% strand | P97227 |
| E, F, G, H | (UNK)(UNK)(UNK)(UNK)(UNK)(MSE)(UNK) | protein | 7 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.72 | 0.80 | 51 | empty |
| 2 | 367 | 0.66 | 0.80 | 33 | empty |
| 3 | 329 | 0.66 | 0.81 | 28 | empty |
| 4 | 345 | 0.64 | 0.79 | 30 | empty |
| 5 | 218 | 0.57 | 0.79 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–C · 374 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 4 hydrogen bonds · protein-protein
- C–G · 301 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 292 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 291 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 2G3V · Crystal structure of CagS (HP0534, Cag13) from Helicobacter pylori · the same entry in another collection · chain H against H, TM-score 1.00
- P97227 · AlphaFold monomer V2.0 prediction for cag pathogenicity island protein 13 (P97227) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P97227
- Elsewhere: RCSB PDB 2G3V · PDBe 2G3V · UniProt P97227
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