MolNFT v1 · #47888 · protein
Crystal structure of a complex between electron transfer partners, cytochrome C peroxidase and cytochrome C
2PCB · Cytochrome C peroxidase (ccp): “Crystal structure of a complex between electron transfer partners, cytochrome C peroxidase and cytochrome C”. X-ray diffraction, 1 ligand (HEM), 6 pockets (best druggability 0.83). MolNFT v1 #47888 on…
- PDB
- 2PCB
- Type
- protein
- Length
- 692 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase (ccp); Cytochrome C
- UniProt
- P00431, P00004
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase (ccp) | protein | 294 | 49% helix, 7% strand | P00431 |
| B | Cytochrome C | protein | 104 | 37% helix, 2% strand | P00004 |
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 | 679 | 0.83 | 0.87 | 78 | HEM |
| 2 | 920 | 0.80 | 0.82 | 80 | empty |
| 3 | 376 | 0.80 | 0.89 | 46 | HEM |
| 4 | 406 | 0.80 | 0.88 | 44 | HEM |
| 5 | 67 | 0.30 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–C · 658 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2PCB · Crystal structure of a complex between electron transfer partners, cytochrome C… · 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 C against A, TM-score 0.99
- P00004 · AlphaFold monomer V2.0 prediction for cytochrome C (P00004) · 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 P00431
- Every structure of UniProt P00004
- Elsewhere: RCSB PDB 2PCB · PDBe 2PCB · UniProt P00431 · UniProt P00004
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