MolNFT v1 · #115395 · protein
Complex of yeast cytochrome C peroxidase (W191G) bound to 3- aminobenzotrifluoride with iso-1 cytochrome C
5CIC · Cytochrome C peroxidase, mitochondrial: “Complex of yeast cytochrome C peroxidase (W191G) bound to 3- aminobenzotrifluoride with iso-1 cytochrome C”. X-ray diffraction, 2 ligands (HEC, 51R), 7 pockets (best druggability 0.87).…
- PDB
- 5CIC
- 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
- HEC, 51R
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 48% 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, D | Cytochrome C iso-1 | protein | 108 | 41% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- 51R · 3-(trifluoromethyl)aniline · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.87 | 0.88 | 99 | empty |
| 2 | 451 | 0.82 | 0.89 | 49 | HEC, 51R |
| 3 | 447 | 0.81 | 0.88 | 50 | HEC, 51R |
| 4 | 504 | 0.77 | 0.84 | 61 | HEC |
| 5 | 249 | 0.74 | 0.88 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 610 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 591 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 279 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 256 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5CIC · Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with… · 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 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 5CIC · PDBe 5CIC · UniProt P00431 · UniProt P00044
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