Research workbench
Structure of the fully oxidized di-heme cytochrome C peroxidase from R. capsulatus
Analyse Structure of the fully oxidized di-heme cytochrome C peroxidase from R.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZZH
- Type
- protein
- Length
- 1,210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase
- EC
- 1.11.1.5
- Ligands
- HEC, ZN, CA
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 297 | 38% helix, 10% strand | — |
| B | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 308 | 37% helix, 9% strand | — |
| C | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 307 | 38% helix, 9% strand | — |
| D | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 298 | 38% helix, 10% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.84 | 0.93 | 43 | CA, HEC |
| 2 | 336 | 0.84 | 0.93 | 41 | CA, HEC |
| 3 | 328 | 0.83 | 0.92 | 41 | HEC |
| 4 | 333 | 0.82 | 0.92 | 40 | CA, HEC |
| 5 | 706 | 0.77 | 0.82 | 70 | HEC |
Interfaces
4 interfaces between chains.
- B–C · 1241 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1191 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 546 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1ZZH · Structure of the fully oxidized di-heme cytochrome c peroxidase from R. capsulatus · 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 1ZZH · PDBe 1ZZH
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