MolNFT v1 · #168861 · protein
The cryo-EM structure of the ubiquinol oxidase from escherichia COLI
6WTI · Cytochrome O ubiquinol oxidase, subunit I: “The cryo-EM structure of the ubiquinol oxidase from escherichia COLI”. Electron microscopy, 6 ligands (3PE, HEM, HEO), 17 pockets (best druggability 0.91). MolNFT v1 #168861 on GenesisL1…
- PDB
- 6WTI
- Type
- protein
- Length
- 1,207 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome O ubiquinol oxidase, subunit I; Ubiquinol oxidase subunit 2; Cytochrome O…
- EC
- 1.10.3.-
- UniProt
- H4KCU1, A0A024L5V9, D6I7E4, I2RK84
- Ligands
- 3PE, HEM, HEO, UQ8, U9V, CU
- Pockets
- 17 · best druggability 0.91
Structure
electron microscopy · 4 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome O ubiquinol oxidase, subunit I (EC 1.10.3.-) | protein | 660 | 70% helix, 2% strand | H4KCU1 |
| B | Ubiquinol oxidase subunit 2 | protein | 262 | 34% helix, 24% strand | A0A024L5V9 |
| C | Cytochrome O ubiquinol oxidase | protein | 186 | 84% helix, 0% strand | D6I7E4 |
| D | Cytochrome O ubiquinol oxidase, subunit IV (EC 1.10.3.-) | protein | 99 | 82% helix, 0% strand | I2RK84 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 9 copies · chains A, C, B, D
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HEO · Heme O · ligand · chains A, B
- UQ8 · Ubiquinone-8 · ligand · chains A
- U9V · pentadecyl(tetradecyl)peroxyanhydride · ligand · chains A
- CU · Copper (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.91 | 0.92 | 108 | HEM, HEO |
| 2 | 1020 | 0.83 | 0.83 | 71 | 3PE |
| 3 | 573 | 0.69 | 0.78 | 74 | UQ8, U9V |
| 4 | 462 | 0.68 | 0.79 | 41 | 3PE |
| 5 | 231 | 0.67 | 0.83 | 23 | 3PE |
Interfaces
5 interfaces between chains.
- A–B · 3765 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1835 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 1313 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 892 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 374 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WTI · The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli · 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 H4KCU1
- Every structure of UniProt A0A024L5V9
- Every structure of UniProt D6I7E4
- Every structure of UniProt I2RK84
- Elsewhere: RCSB PDB 6WTI · PDBe 6WTI · UniProt H4KCU1 · UniProt A0A024L5V9 · UniProt D6I7E4 · UniProt I2RK84
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