MolNFT v1 · #159879 · protein
Yeast cytochrome C peroxidase in complex with iso-1 cytochrome C (Y48K)
6P43 · Cytochrome C peroxidase, mitochondrial: “Yeast cytochrome C peroxidase in complex with iso-1 cytochrome C (Y48K)”. X-ray diffraction, 1 ligand (HEM), 6 pockets (best druggability 0.80). MolNFT v1 #159879 on GenesisL1: 3D structure…
- PDB
- 6P43
- Type
- protein
- Length
- 696 residues
- Chains
- 3
- 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
- HEM
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 294 | 50% helix, 8% strand | P00431 |
| B | Cytochrome C iso-1 | protein | 108 | 35% helix, 2% strand | P00044 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.80 | 0.89 | 44 | HEM |
| 2 | 494 | 0.79 | 0.86 | 53 | HEM |
| 3 | 537 | 0.75 | 0.83 | 69 | HEM |
| 4 | 284 | 0.75 | 0.88 | 37 | empty |
| 5 | 173 | 0.45 | 0.75 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 608 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (heme attachment).
Compared structures
- 6P43 · Yeast cytochrome c peroxidase in complex with iso-1 cytochrome c (Y48K) · the same entry in another collection · chain A against A, TM-score 1.00
- P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · a predicted model of the same protein · chain A 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 0.95
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 6P43 · PDBe 6P43 · UniProt P00431 · UniProt P00044
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