MolNFT v1 · #21340 · protein
Structure of a cytochrome C peroxidase-cytochrome C site specific cross-link
1S6V · Cytochrome C peroxidase, mitochondrial: “Structure of a cytochrome C peroxidase-cytochrome C site specific cross-link”. X-ray diffraction, 2 ligands (HEC, IOD), 8 pockets (best druggability 0.89). MolNFT v1 #21340 on GenesisL1: 3D…
- PDB
- 1S6V
- 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, IOD
- Pockets
- 8 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 48% 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, 7% strand | P00431 |
| B, D | Cytochrome C, iso-1 | protein | 108 | 43% helix, 2% strand | P00044 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.89 | 0.91 | 121 | HEC |
| 2 | 248 | 0.81 | 0.93 | 45 | HEC |
| 3 | 384 | 0.80 | 0.89 | 44 | HEC |
| 4 | 387 | 0.79 | 0.88 | 43 | HEC |
| 5 | 203 | 0.73 | 0.89 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–C · 499 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 302 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, heme c attachment).
Compared structures
- 1S6V · Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link · 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 0.99
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 P00044
- Elsewhere: RCSB PDB 1S6V · PDBe 1S6V · UniProt P00431 · UniProt P00044
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