MolNFT v1 · #184662 · protein
High resolution structure of cytochrome bd-II oxidase from E. COLI
7OY2 · Appb protein: “High resolution structure of cytochrome bd-II oxidase from E. COLI”. Electron microscopy, 6 ligands (HEB, CDN, DK8), 10 pockets (best druggability 0.87). MolNFT v1 #184662 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7OY2
- Type
- protein
- Length
- 858 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Appb protein; Cytochrome bd-II ubiquinol oxidase subunit 1; Cytochrome bd-II oxidase…
- EC
- 1.10.3.10, 1.10.3.-, 7.1.1.3
- UniProt
- W8T4P7, P26459, A0A4S5AYP7
- Ligands
- HEB, CDN, DK8, POV, HDD, OXY
- Pockets
- 10 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 78% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Appb protein (EC 1.10.3.10, 1.10.3.-) | protein | 376 | 74% helix, 7% strand | W8T4P7 |
| C | Cytochrome bd-II ubiquinol oxidase subunit 1 (EC 7.1.1.3) | protein | 454 | 81% helix, 3% strand | P26459 |
| X | Cytochrome bd-II oxidase subunit cbdx | protein | 28 | 82% helix, 0% strand | A0A4S5AYP7 |
Ligands and binding sites
- HEB · Heme B/C · ligand · 2 copies · chains C
- CDN · Cardiolipin · ligand · chains B
- DK8 · 2-[(2~{E},6~{E},10~{Z},14~{E},18~{E},22~{E},26~{E})-3, 7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14, 18,22,26,30-octaenyl]naphthalene-1,4-dione · ligand · chains B
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains C
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains B, C
- OXY · Oxygen molecule · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.87 | 0.92 | 64 | DK8 |
| 2 | 608 | 0.85 | 0.90 | 69 | HEB, HDD, OXY |
| 3 | 232 | 0.80 | 0.93 | 37 | HEB |
| 4 | 192 | 0.62 | 0.83 | 34 | empty |
| 5 | 133 | 0.59 | 0.84 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–C · 3569 Ų buried · 35 hydrogen bonds · protein-protein
- C–X · 1278 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7OY2 · High resolution structure of cytochrome bd-II oxidase from E. coli · the same entry in another collection · chain B against B, TM-score 1.00
- P26459 · AlphaFold monomer V2.0 prediction for cytochrome bd-II ubiquinol oxidase subunit 1… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 W8T4P7
- Every structure of UniProt P26459
- Every structure of UniProt A0A4S5AYP7
- Elsewhere: RCSB PDB 7OY2 · PDBe 7OY2 · UniProt W8T4P7 · UniProt P26459 · UniProt A0A4S5AYP7
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