Research workbench
Three dimensional structure of the reduced form of nine-heme cytochrome C at pH 7.5
Analyse Three dimensional structure of the reduced form of nine-heme cytochrome C at pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OFY
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nine heme cytochrome C
- UniProt
- Q9RN68
- Ligands
- HEC
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nine heme cytochrome C | protein | 292 | 39% helix, 6% strand | Q9RN68 |
Ligands and binding sites
- HEC · Heme C · ligand · 18 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.89 | 0.91 | 149 | HEC |
| 2 | 1101 | 0.89 | 0.91 | 147 | HEC |
| 3 | 64 | 0.62 | 0.92 | 21 | empty |
| 4 | 89 | 0.56 | 0.86 | 18 | HEC |
| 5 | 53 | 0.55 | 0.90 | 16 | HEC |
Interfaces
1 interface between chains.
- A–B · 1336 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 cofactor (heme c attachment).
Compared structures
- 1OFY · three dimensional structure of the reduced form of nine-heme cytochrome c at ph 7.5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RN68 · AlphaFold monomer V2.0 prediction for nine-heme cytochrome C (Q9RN68) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9RN68
- Elsewhere: RCSB PDB 1OFY · PDBe 1OFY · UniProt Q9RN68
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