Research workbench
Crystal structure of the di-haem cytochrome C peroxidase from paracoccus pantotrophus - oxidised form
Analyse Crystal structure of the di-haem cytochrome C peroxidase from paracoccus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C1U
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- 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
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-haem cytochrome C peroxidase (EC 1.11.1.5) | protein | 329 | 37% helix, 10% strand | — |
| B | Di-haem cytochrome C peroxidase (EC 1.11.1.5) | protein | 324 | 37% helix, 10% strand | — |
| C | Di-haem cytochrome C peroxidase (EC 1.11.1.5) | protein | 329 | 37% helix, 9% strand | — |
| D | Di-haem cytochrome C peroxidase (EC 1.11.1.5) | protein | 322 | 39% helix, 10% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.86 | 0.87 | 100 | HEC, CA |
| 2 | 868 | 0.86 | 0.88 | 103 | HEC |
| 3 | 1135 | 0.85 | 0.86 | 149 | HEC |
| 4 | 300 | 0.84 | 0.94 | 42 | HEC, CA |
| 5 | 825 | 0.80 | 0.83 | 104 | HEC |
Interfaces
5 interfaces between chains.
- A–B · 1339 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1324 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 201 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 120 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme c attachment).
Compared structures
- 2C1U · Crystal structure of the di-haem cytochrome C peroxidase from paracoccus pantotrophus… · the same entry in another collection · chain C against C, 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 2C1U · PDBe 2C1U
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