Research workbench
The structure of CBB3 cytochrome oxidase.
Analyse The structure of CBB3 cytochrome oxidase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
- Molecule
- Cbb3-type cytochrome c oxidase subunit CcoN1; Cbb3-type cytochrome c oxidase subunit II…
- EC
- 1.9.3.1
- UniProt
- D9IA43, D9IA44, D9IA45, H7ESS5
- Ligands
- HEC, HEM, PEO, FC6, CA, CU, PO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · resolution 3.2 · 6 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cbb3-type cytochrome c oxidase subunit CcoN1 (EC 1.9.3.1) | protein | 466 | 75% helix, 3% strand | D9IA43 |
| B, E, H, L | Cbb3-type cytochrome c oxidase subunit II | protein | 197 | 45% helix, 2% strand | D9IA44 |
| C, F, I, M | Cbb3-type cytochrome c oxidase subunit CcoP1 | protein | 303 | 55% helix, 5% strand | D9IA45 |
| D | Cbb3-type cytochrome c oxidase subunit CcoN1 (EC 1.9.3.1) | protein | 463 | 76% helix, 3% strand | D9IA43 |
| G, K | Cbb3-type cytochrome c oxidase subunit CcoN1 (EC 1.9.3.1) | protein | 465 | 76% helix, 3% strand | D9IA43 |
| N, O, P, Q | Putative uncharacterized protein | protein | 29 | 83% helix, 0% strand | 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.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.90 | 0.92 | 124 | HEC, FC6 |
| 2 | 768 | 0.90 | 0.93 | 109 | HEC |
| 3 | 524 | 0.88 | 0.94 | 70 | HEM, PEO, CA |
| 4 | 382 | 0.87 | 0.96 | 67 | HEC |
| 5 | 496 | 0.87 | 0.94 | 68 | HEM, PEO, CA |
Interfaces
30 interfaces between chains.
- G–H · 3764 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3760 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 3746 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 3731 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2558 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (heme c attachment).
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.