Research workbench
K13R mutant of horse cytochrome C and yeast cytochrome C peroxidase complex
Analyse K13R mutant of horse cytochrome C and yeast cytochrome C peroxidase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NFG
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase, mitochondrial; Cytochrome C
- EC
- 1.11.1.5
- UniProt
- P00431, P00004
- Ligands
- HEM, HEC, UNX
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 293 | 49% helix, 7% strand | P00431 |
| B | Cytochrome C | protein | 104 | 40% helix, 2% strand | P00004 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HEC · Heme C · ligand · chains A, B
- UNX · Unknown atom or ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.82 | 0.86 | 94 | HEC |
| 2 | 377 | 0.80 | 0.89 | 45 | HEM, UNX |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme c attachment).
Compared structures
- 4NFG · K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex · the same entry in another collection · chain A against A, 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
- P00004 · AlphaFold monomer V2.0 prediction for cytochrome C (P00004) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P00004
- Elsewhere: RCSB PDB 4NFG · PDBe 4NFG · UniProt P00431 · UniProt P00004
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.