MolNFT v1 · #32823 · protein
Crystal structure of the di-haem cytochrome C peroxidase from paracoccus pantotrophus - mixed valence form
2C1V: “Crystal structure of the di-haem cytochrome C peroxidase from paracoccus pantotrophus - mixed valence form”. X-ray diffraction, 2 ligands (HEC, CA), 9 pockets (best druggability 0.86). MolNFT v1 #32823 on GenesisL1: 3D structure…
- PDB
- 2C1V
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-haem cytochrome C peroxidase
- EC
- 1.11.1.5
- Ligands
- HEC, CA
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Di-haem cytochrome C peroxidase (EC 1.11.1.5) | protein | 335 | 40% helix, 7% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.86 | 0.92 | 81 | HEC, EDO |
| 2 | 275 | 0.83 | 0.94 | 44 | HEC |
| 3 | 134 | 0.79 | 0.97 | 32 | empty |
| 4 | 243 | 0.76 | 0.90 | 39 | HEC |
| 5 | 227 | 0.62 | 0.82 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1714 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 2C1V · CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 2C1V · PDBe 2C1V
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.