Research workbench
Structure of the helicobacter pylori caga oncogene bound to the human tumor suppressor apoptosis-stimulating protein of P53-2
Analyse Structure of the helicobacter pylori caga oncogene bound to the human tumor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IRV
- Type
- protein
- Length
- 861 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxicity-associated immunodominant antigen; Apoptosis-stimulating of P53 protein 2
- UniProt
- P55980, Q13625
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxicity-associated immunodominant antigen | protein | 197 | 81% helix, 0% strand | P55980 |
| B | Cytotoxicity-associated immunodominant antigen | protein | 194 | 81% helix, 0% strand | P55980 |
| C | Cytotoxicity-associated immunodominant antigen | protein | 192 | 82% helix, 0% strand | P55980 |
| D | Cytotoxicity-associated immunodominant antigen | protein | 198 | 82% helix, 0% strand | P55980 |
| E, F, G, H | Apoptosis-stimulating of P53 protein 2 | protein | 20 | 70% helix, 0% strand | Q13625 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.75 | 0.87 | 35 | empty |
| 2 | 648 | 0.67 | 0.76 | 54 | empty |
| 3 | 335 | 0.53 | 0.74 | 32 | empty |
| 4 | 91 | 0.49 | 0.82 | 19 | empty |
| 5 | 95 | 0.42 | 0.78 | 17 | empty |
Interfaces
9 interfaces between chains.
- B–F · 1086 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 1062 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 1057 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 1054 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1051 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4IRV · Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor… · the same entry in another collection · chain H against H, TM-score 1.00
- P55980 · AlphaFold monomer V2.0 prediction for cytotoxicity-associated immunodominant antigen… · a predicted model of the same protein · chain C 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 P55980
- Every structure of UniProt Q13625
- Elsewhere: RCSB PDB 4IRV · PDBe 4IRV · UniProt P55980 · UniProt Q13625
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