Research workbench
Cryo-EM structure of the E. COLI cytochrome bd-I oxidase at 2.68 a resolution
Analyse Cryo-EM structure of the E. COLI cytochrome bd-I oxidase at 2.68 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RKO
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome bd-I ubiquinol oxidase subunit 2; Cytochrome bd-I ubiquinol oxidase subunit 1…
- EC
- 7.1.1.7
- UniProt
- P0ABK2, P0ABJ9, A5A618, P56100
- Ligands
- POV, HEB, UQ8, HDD, OXY
- Pockets
- 12 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 75% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cytochrome bd-I ubiquinol oxidase subunit 2 (EC 7.1.1.7) | protein | 378 | 69% helix, 6% strand | P0ABK2 |
| A | Cytochrome bd-I ubiquinol oxidase subunit 1 (EC 7.1.1.7) | protein | 444 | 79% helix, 3% strand | P0ABJ9 |
| H | Uncharacterized protein ynhf | protein | 27 | 89% helix, 0% strand | A5A618 |
| X | Cytochrome bd-I ubiquinol oxidase subunit X (EC 7.1.1.7) | protein | 26 | 85% helix, 0% strand | P56100 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains B, A, H
- HEB · Heme B/C · ligand · 2 copies · chains A, H
- UQ8 · Ubiquinone-8 · ligand · chains B
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains B, A
- OXY · Oxygen molecule · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.88 | 0.92 | 57 | HDD, HEB, OXY |
| 2 | 738 | 0.88 | 0.91 | 78 | UQ8 |
| 3 | 547 | 0.75 | 0.81 | 38 | POV |
| 4 | 443 | 0.74 | 0.83 | 53 | empty |
| 5 | 340 | 0.72 | 0.84 | 33 | HEB |
Interfaces
3 interfaces between chains.
- B–A · 3534 Ų buried · 25 hydrogen bonds · protein-protein
- A–X · 1023 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 993 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6RKO · Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution · the same entry in another collection · chain X against X, 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
- A5A618 · AlphaFold monomer V2.0 prediction for uncharacterized protein ynhf (A5A618) · a predicted model of the same protein · chain H against A, TM-score 0.72
- P56100 · AlphaFold monomer V2.0 prediction for cytochrome bd-I ubiquinol oxidase subunit X (P56100) · a predicted model of the same protein · chain X against A, TM-score 0.69
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 P0ABK2
- Every structure of UniProt P0ABJ9
- Every structure of UniProt A5A618
- Every structure of UniProt P56100
- Elsewhere: RCSB PDB 6RKO · PDBe 6RKO · UniProt P0ABK2 · UniProt P0ABJ9 · UniProt A5A618 · UniProt P56100
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