MolNFT v1 · #6539 · protein
The structure of ubiquinol oxidase from escherichia COLI
1FFT: “The structure of ubiquinol oxidase from escherichia COLI”. X-ray diffraction, 3 ligands (HEM, HEO, CU), 20 pockets (best druggability 0.90). MolNFT v1 #6539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FFT
- Type
- protein
- Length
- 2,104 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol oxidase
- EC
- 1.10.3.-
- UniProt
- P0ABI8, P0ABJ1, P0ABJ3
- Ligands
- HEM, HEO, CU
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ubiquinol oxidase (EC 1.10.3.-) | protein | 501 | 67% helix, 0% strand | P0ABI8 |
| B, G | Ubiquinol oxidase (EC 1.10.3.-) | protein | 257 | 28% helix, 19% strand | P0ABJ1 |
| C, H | Ubiquinol oxidase (EC 1.10.3.-) | protein | 185 | 64% helix, 0% strand | P0ABJ3 |
| D, I | Ubiquinol oxidase (EC 1.10.3.-) | protein | 109 | 79% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, F
- HEO · Heme O · ligand · 2 copies · chains A, B, F, G
- CU · Copper (II) ion · metal · 2 copies · chains A, F
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 | 1189 | 0.90 | 0.92 | 144 | CU, HEM, HEO |
| 2 | 1192 | 0.90 | 0.92 | 137 | HEM, HEO |
| 3 | 173 | 0.71 | 0.89 | 40 | empty |
| 4 | 616 | 0.71 | 0.78 | 71 | empty |
| 5 | 551 | 0.70 | 0.79 | 64 | empty |
Interfaces
10 interfaces between chains.
- F–G · 3470 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3417 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 1357 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1182 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 1053 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1FFT · The structure of ubiquinol oxidase from Escherichia coli · the same entry in another collection · chain I against I, TM-score 1.00
- P0ABI8 · AlphaFold monomer V2.0 prediction for cytochrome BO(3) ubiquinol oxidase subunit 1… · a predicted model of the same protein · chain F against A, TM-score 0.97
- P0ABJ1 · AlphaFold monomer V2.0 prediction for cytochrome BO(3) ubiquinol oxidase subunit 2… · a predicted model of the same protein · chain G against A, TM-score 0.94
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 P0ABI8
- Every structure of UniProt P0ABJ1
- Every structure of UniProt P0ABJ3
- Elsewhere: RCSB PDB 1FFT · PDBe 1FFT · UniProt P0ABI8 · UniProt P0ABJ1 · UniProt P0ABJ3
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