MolNFT v1 · #110394 · protein
Crystal structure of wild type cytochrome C peroxidase
4XVA · Cytochrome C peroxidase, mitochondrial: “Crystal structure of wild type cytochrome C peroxidase”. X-ray diffraction, 2 ligands (HEM, BZI), 12 pockets (best druggability 0.82). MolNFT v1 #110394 on GenesisL1: 3D structure, binding…
- PDB
- 4XVA
- Type
- protein
- Length
- 1,170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase, mitochondrial
- EC
- 1.11.1.5
- UniProt
- P00431
- Ligands
- HEM, BZI
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 293 | 48% helix, 8% strand | P00431 |
| C, G | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 292 | 50% helix, 7% strand | P00431 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, E, G
- BZI · Benzimidazole · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.82 | 0.90 | 46 | HEM |
| 2 | 394 | 0.81 | 0.89 | 44 | HEM |
| 3 | 430 | 0.80 | 0.88 | 46 | HEM |
| 4 | 386 | 0.80 | 0.89 | 44 | HEM |
| 5 | 1030 | 0.78 | 0.80 | 87 | empty |
Interfaces
3 interfaces between chains.
- C–E · 547 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 340 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4XVA · Crystal structure of wild type cytochrome c peroxidase · the same entry in another collection · chain G against G, TM-score 1.00
- P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · a predicted model of the same protein · chain E against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 4XVA · PDBe 4XVA · UniProt P00431
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