Research workbench
Complex of yeast cytochrome C peroxidase (W191Y) with iso-1 cytochrome C
Analyse Complex of yeast cytochrome C peroxidase (W191Y) with iso-1 cytochrome C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIH
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase, mitochondrial; Cytochrome C iso-1
- EC
- 1.11.1.5
- UniProt
- P00431, P00044
- Ligands
- HEC
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 294 | 39% helix, 8% strand | P00431 |
| B, D | Cytochrome C iso-1 | protein | 103 | 31% helix, 0% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.87 | 0.88 | 111 | empty |
| 2 | 467 | 0.81 | 0.88 | 47 | HEC |
| 3 | 538 | 0.81 | 0.87 | 72 | HEC |
| 4 | 387 | 0.81 | 0.89 | 47 | HEC |
| 5 | 609 | 0.79 | 0.84 | 71 | HEC |
Interfaces
5 interfaces between chains.
- C–D · 680 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 598 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 231 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 220 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5CIH · Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c · the same entry in another collection · chain D against D, TM-score 1.00
- P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.93
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 P00431
- Every structure of UniProt P00044
- Elsewhere: RCSB PDB 5CIH · PDBe 5CIH · UniProt P00431 · UniProt P00044
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