MolNFT v1 · #184504 · protein
Cytochrome bd-II type oxidase with bound aurachin D
7OSE · Cytochrome bd-II ubiquinol oxidase subunit 1: “Cytochrome bd-II type oxidase with bound aurachin D”. Electron microscopy, 4 ligands (HEB, HDD, 0NI), 20 pockets (best druggability 0.88). MolNFT v1 #184504 on GenesisL1: 3D structure…
- PDB
- 7OSE
- Type
- protein
- Length
- 1,816 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome bd-II ubiquinol oxidase subunit 1; Appb protein; Putative cytochrome bd-II…
- EC
- 7.1.1.3, 1.10.3.10, 1.10.3.-
- UniProt
- P26459, W8T4P7, P24244
- Ligands
- HEB, HDD, 0NI, UQ8
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytochrome bd-II ubiquinol oxidase subunit 1 (EC 7.1.1.3) | protein | 503 | 72% helix, 4% strand | P26459 |
| B, E | Appb protein (EC 1.10.3.10, 1.10.3.-) | protein | 377 | 72% helix, 6% strand | W8T4P7 |
| C, F | Putative cytochrome bd-II ubiquinol oxidase subunit appx | protein | 28 | 82% helix, 0% strand | P24244 |
Ligands and binding sites
- HEB · Heme B/C · ligand · 4 copies · chains A, D
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 2 copies · chains A, B, D, E
- 0NI · Aurachin D · ligand · 2 copies · chains A, D
- UQ8 · Ubiquinone-8 · ligand · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.88 | 0.91 | 61 | UQ8 |
| 2 | 726 | 0.87 | 0.90 | 62 | UQ8 |
| 3 | 691 | 0.87 | 0.90 | 58 | HEB, HDD |
| 4 | 696 | 0.87 | 0.90 | 57 | HEB, HDD |
| 5 | 400 | 0.80 | 0.88 | 49 | HEB, 0NI |
Interfaces
7 interfaces between chains.
- A–B · 3597 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 3595 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1302 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1301 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 615 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7OSE · cytochrome bd-II type oxidase with bound aurachin D · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.99
- P24244 · AlphaFold monomer V2.0 prediction for putative cytochrome bd-II ubiquinol oxidase subunit… · a predicted model of the same protein · chain F against A, TM-score 0.83
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 P26459
- Every structure of UniProt W8T4P7
- Every structure of UniProt P24244
- Elsewhere: RCSB PDB 7OSE · PDBe 7OSE · UniProt P26459 · UniProt W8T4P7 · UniProt P24244
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.