Research workbench
The structure of bd oxidase from escherichia COLI
Analyse The structure of bd oxidase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RX4
- Type
- protein
- Length
- 910 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome bd-I ubiquinol oxidase subunit 1; Cytochrome bd-I ubiquinol oxidase subunit 2…
- EC
- 7.1.1.7
- UniProt
- P0ABJ9, P0ABK2, P56100
- Ligands
- HEB, HDD, PEE, UQ8
- Pockets
- 12 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome bd-I ubiquinol oxidase subunit 1 (EC 7.1.1.7) | protein | 474 | 76% helix, 3% strand | P0ABJ9 |
| B | Cytochrome bd-I ubiquinol oxidase subunit 2 (EC 7.1.1.7) | protein | 379 | 68% helix, 3% strand | P0ABK2 |
| C | Cytochrome bd-I ubiquinol oxidase subunit X (EC 7.1.1.7) | protein | 31 | 87% helix, 0% strand | P56100 |
| D | Cytochrome bd-I ubiquinol oxidase subunit Y | protein | 26 | 85% helix, 0% strand | — |
Ligands and binding sites
- HEB · Heme B/C · ligand · 2 copies · chains A, D
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains A, B
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · chains B
- UQ8 · Ubiquinone-8 · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.88 | 0.92 | 62 | HEB, HDD |
| 2 | 701 | 0.87 | 0.90 | 71 | UQ8 |
| 3 | 397 | 0.80 | 0.89 | 39 | HEB |
| 4 | 360 | 0.73 | 0.85 | 47 | empty |
| 5 | 470 | 0.72 | 0.81 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3757 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1194 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 712 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RX4 · The structure of bd oxidase from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABK2 · AlphaFold monomer V2.0 prediction for cytochrome bd-I ubiquinol oxidase subunit 2 (P0ABK2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0ABJ9 · AlphaFold monomer V2.0 prediction for cytochrome bd-I ubiquinol oxidase subunit 1 (P0ABJ9) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P56100 · AlphaFold monomer V2.0 prediction for cytochrome bd-I ubiquinol oxidase subunit X (P56100) · a predicted model of the same protein · chain C against A, TM-score 0.75
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 P0ABJ9
- Every structure of UniProt P0ABK2
- Every structure of UniProt P56100
- Elsewhere: RCSB PDB 6RX4 · PDBe 6RX4 · UniProt P0ABJ9 · UniProt P0ABK2 · UniProt P56100
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