Research workbench
Complex of yeast cytochrome C peroxidase (W191G) bound to 2,4- dimethylaniline with iso-1 cytochrome C
Analyse Complex of yeast cytochrome C peroxidase (W191G) bound to 2,4- dimethylaniline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIB
- 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, 51S
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 294 | 44% helix, 7% strand | P00431 |
| B, D | Cytochrome C iso-1 | protein | 108 | 33% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- 51S · 2,4-dimethylaniline · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.83 | 0.90 | 51 | HEC, 51S |
| 2 | 1078 | 0.80 | 0.82 | 100 | empty |
| 3 | 496 | 0.80 | 0.87 | 55 | HEC, 51S |
| 4 | 648 | 0.79 | 0.84 | 85 | HEC |
| 5 | 424 | 0.78 | 0.86 | 59 | HEC |
Interfaces
5 interfaces between chains.
- A–B · 610 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 544 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 264 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5CIB · Complex of yeast cytochrome c peroxidase (W191G) bound to 2,4-dimethylaniline with iso-1… · 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 B against A, TM-score 0.97
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 5CIB · PDBe 5CIB · UniProt P00431 · UniProt P00044
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