Research workbench
The X-ray structure of the primary adduct formed in the reaction between cisplatin and cytochrome C
Analyse The X-ray structure of the primary adduct formed in the reaction between… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RSZ
- Type
- protein
- Length
- 624 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- P00004
- Ligands
- HEC, CPT, NO3, SO4
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cytochrome C | protein | 104 | 41% helix, 2% strand | P00004 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, B, C, D, E, F
- CPT · Cisplatin · ligand · 5 copies · chains A, B, D, E, F
- NO3 · Nitrate ion · ion · 16 copies · chains A, C, B, D, F, E
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.87 | 0.88 | 123 | NO3, HEC |
| 2 | 255 | 0.81 | 0.93 | 47 | HEC, NO3 |
| 3 | 411 | 0.79 | 0.88 | 64 | HEC, NO3 |
| 4 | 167 | 0.75 | 0.91 | 30 | HEC |
| 5 | 171 | 0.74 | 0.91 | 30 | HEC |
Interfaces
9 interfaces between chains.
- D–F · 624 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 607 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 597 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (heme c attachment).
Compared structures
- 4RSZ · The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and… · the same entry in another collection · chain F against F, TM-score 1.00
- P00004 · AlphaFold monomer V2.0 prediction for cytochrome C (P00004) · 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 P00004
- Elsewhere: RCSB PDB 4RSZ · PDBe 4RSZ · UniProt P00004
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