Research workbench
Crystal structure of a complex between electron transfer partners, cytochrome C peroxidase and cytochrome C
Analyse Crystal structure of a complex between electron transfer partners, cytochrome C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PCC
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase; Iso-1-cytochrome C
- UniProt
- P00431, P00044
- Ligands
- HEM, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase | protein | 294 | 50% helix, 7% strand | P00431 |
| B, D | Iso-1-cytochrome C | protein | 108 | 38% helix, 2% strand | P00044 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.84 | 0.89 | 64 | empty |
| 2 | 406 | 0.81 | 0.89 | 44 | SO4, HEM |
| 3 | 410 | 0.80 | 0.88 | 44 | SO4, HEM |
| 4 | 213 | 0.77 | 0.92 | 29 | empty |
| 5 | 432 | 0.77 | 0.86 | 66 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 633 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 596 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 416 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 159 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2PCC · Crystal structure of a complex between electron transfer partners, 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 D 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 P00044
- Elsewhere: RCSB PDB 2PCC · PDBe 2PCC · UniProt P00431 · UniProt P00044
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