Research workbench
Cytochrome C peroxidase bccp of shewanella oneidensis
Analyse Cytochrome C peroxidase bccp of shewanella oneidensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O5C
- Type
- protein
- Length
- 1,226 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C551 peroxidase
- UniProt
- Q8EF24
- Ligands
- HEM, CA
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C551 peroxidase | protein | 308 | 40% helix, 5% strand | Q8EF24 |
| B, D | Cytochrome C551 peroxidase | protein | 307 | 41% helix, 5% strand | Q8EF24 |
| C | Cytochrome C551 peroxidase | protein | 304 | 41% helix, 5% strand | Q8EF24 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- BU3 · (R,R)-2,3-butanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.86 | 0.91 | 77 | HEM, CA |
| 2 | 587 | 0.86 | 0.90 | 78 | HEM |
| 3 | 534 | 0.85 | 0.91 | 74 | HEM, CA |
| 4 | 264 | 0.83 | 0.94 | 42 | HEM |
| 5 | 170 | 0.82 | 0.97 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1977 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1962 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 180 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 cofactor (heme attachment).
Compared structures
- 3O5C · Cytochrome c Peroxidase BccP of Shewanella oneidensis · 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
- Every structure of UniProt Q8EF24
- Elsewhere: RCSB PDB 3O5C · PDBe 3O5C · UniProt Q8EF24
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