MolNFT v2 · #116928 · protein
The structure of CBB3 cytochrome oxidase.
5DJQ: “The structure of CBB3 cytochrome oxidase.”. X-ray diffraction at 3.2, 7 ligands (HEC, HEM, PEO). MolNFT v2 #116928 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DJQ
- Type
- protein
- Length
- 3,975 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Pseudomonas stutzeri; Pseudomonas stutzeri ATCC 14405 = CCUG 16156
- UniProt
- D9IA43, D9IA44, D9IA45, H7ESS5
- Ligands
- HEC, HEM, PEO, FC6, CA, CU, PO4
Structure
x-ray diffraction · resolution 3.2 · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 466 | — | D9IA43 |
| B, E, H, L | — | protein | 197 | — | D9IA44 |
| C, F, I, M | — | protein | 303 | — | D9IA45 |
| D | — | protein | 463 | — | D9IA43 |
| G, K | — | protein | 465 | — | D9IA43 |
| N, O, P, Q | — | protein | 29 | — | H7ESS5 |
Ligands and binding sites
- HEC · Heme C · ligand · 12 copies · chains A, B, C, I, D, E, F, G, H, K, L, M
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, D, E, G, H, K, L
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, D, G, K
- FC6 · Hexacyanoferrate(3-) · ligand · 4 copies · chains C, M, F, I
- CA · Calcium ion · metal · 8 copies · chains A, B, D, E, G, H, K, L
- CU · Copper (II) ion · metal · 4 copies · chains A, D, G, K
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, F, G, I, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DJQ · The structure of CBB3 cytochrome oxidase. · the same entry in another collection · chain Q against Q, 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 D9IA43
- Every structure of UniProt D9IA44
- Every structure of UniProt D9IA45
- Every structure of UniProt H7ESS5
- Elsewhere: RCSB PDB 5DJQ · PDBe 5DJQ · UniProt D9IA43 · UniProt D9IA44 · UniProt D9IA45 · UniProt H7ESS5
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