Research workbench
Electron transfer complexes: experimental mapping of the redox- dependent cytochrome C electrostatic surface
Analyse Electron transfer complexes: experimental mapping of the redox- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O1Y
- Type
- protein
- Length
- 312 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- P00004
- Ligands
- ACE, HEC, NO3
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytochrome C | protein | 104 | 40% helix, 2% strand | P00004 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, B, C
- HEC · Heme C · ligand · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 22 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.76 | 0.92 | 34 | HEC |
| 2 | 190 | 0.75 | 0.90 | 35 | HEC |
| 3 | 172 | 0.74 | 0.90 | 35 | HEC |
| 4 | 65 | 0.36 | 0.78 | 16 | empty |
| 5 | 84 | 0.35 | 0.75 | 20 | NO3 |
Interfaces
2 interfaces between chains.
- B–C · 232 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 3 covalent (heme c attachment, covalent ligand).
Compared structures
- 3O1Y · Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c… · the same entry in another collection · chain A against A, 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 3O1Y · PDBe 3O1Y · UniProt P00004
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