MolNFT v1 · #31624 · protein
Crystal structure of the protein-protein complex between F82S cytochrome C and cytochrome C peroxidase
2B10 · Cytochrome C peroxidase, mitochondrial: “Crystal structure of the protein-protein complex between F82S cytochrome C and cytochrome C peroxidase”. X-ray diffraction, 2 ligands (ZNH, HEM), 9 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 2B10
- Type
- protein
- Length
- 804 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
- ZNH, HEM
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 294 | 50% helix, 6% strand | P00431 |
| B, D | Cytochrome C iso-1 | protein | 108 | 37% helix, 2% strand | P00044 |
Ligands and binding sites
- ZNH · Protoporphyrin IX containing Zn · ligand · 2 copies · chains A, C
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 98 | empty |
| 2 | 397 | 0.81 | 0.89 | 47 | ZNH |
| 3 | 397 | 0.80 | 0.89 | 44 | ZNH |
| 4 | 365 | 0.79 | 0.88 | 55 | HEM |
| 5 | 413 | 0.78 | 0.87 | 58 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 738 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2B10 · Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome… · 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 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 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 2B10 · PDBe 2B10 · UniProt P00431 · UniProt P00044
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