Research workbench
Crystal structure of an oxidized form of yeast iso-1-cytochrome C at pH 8.8
Analyse Crystal structure of an oxidized form of yeast iso-1-cytochrome C at pH 8.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MU8
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEC, SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C iso-1 | protein | 107 | 40% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- TBU · Tertiary-butyl alcohol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.79 | 0.93 | 34 | HEC |
| 2 | 220 | 0.79 | 0.92 | 31 | HEC |
| 3 | 94 | 0.34 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 285 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 4MU8 · Crystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8 · the same entry in another collection · chain A against A, TM-score 1.00
- P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00044
- Elsewhere: RCSB PDB 4MU8 · PDBe 4MU8 · UniProt P00044
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