Research workbench
2.55-ångström cryo-EM structure of cytochrome BO3 from escherichia COLI in native membrane
Analyse 2.55-ångström cryo-EM structure of cytochrome BO3 from escherichia COLI in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CUB
- Type
- protein
- Length
- 1,199 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome BO(3) ubiquinol oxidase subunit 1; Cytochrome BO(3) ubiquinol oxidase subunit…
- EC
- 7.1.1.3
- UniProt
- P0ABI8, P0ABJ1, P0ABJ3, P0ABJ6
- Ligands
- 3PE, HEM, HEO, UQ8, CU
- Pockets
- 19 · best druggability 0.90
Structure
electron microscopy · 4 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome BO(3) ubiquinol oxidase subunit 1 (EC 7.1.1.3) | protein | 659 | 67% helix, 2% strand | P0ABI8 |
| B | Cytochrome BO(3) ubiquinol oxidase subunit 2 | protein | 259 | 34% helix, 24% strand | P0ABJ1 |
| C | Cytochrome BO(3) ubiquinol oxidase subunit 3 | protein | 184 | 82% helix, 0% strand | P0ABJ3 |
| D | Cytochrome BO(3) ubiquinol oxidase subunit 4 | protein | 97 | 75% helix, 2% strand | P0ABJ6 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 5 copies · chains A, C
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- HEO · Heme O · ligand · chains A, B
- UQ8 · Ubiquinone-8 · 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
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.90 | 0.92 | 100 | HEM, HEO |
| 2 | 1156 | 0.84 | 0.84 | 74 | 3PE |
| 3 | 259 | 0.67 | 0.83 | 29 | empty |
| 4 | 351 | 0.65 | 0.79 | 33 | empty |
| 5 | 200 | 0.64 | 0.84 | 28 | UQ8 |
Interfaces
5 interfaces between chains.
- A–B · 3748 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1709 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 1317 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 933 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7CUB · 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane · the same entry in another collection · chain D against D, 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 A against A, TM-score 1.00
- P0ABJ1 · AlphaFold monomer V2.0 prediction for cytochrome BO(3) ubiquinol oxidase subunit 2… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P0ABJ3 · AlphaFold monomer V2.0 prediction for cytochrome BO(3) ubiquinol oxidase subunit 3… · a predicted model of the same protein · chain C against A, TM-score 0.89
- P0ABJ6 · AlphaFold monomer V2.0 prediction for cytochrome BO(3) ubiquinol oxidase subunit 4… · a predicted model of the same protein · chain D against A, TM-score 0.66
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
- Every structure of UniProt P0ABJ6
- Elsewhere: RCSB PDB 7CUB · PDBe 7CUB · UniProt P0ABI8 · UniProt P0ABJ1 · UniProt P0ABJ3 · UniProt P0ABJ6
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