Research workbench
E. COLI cytochrome BO3 in msp nanodisc
Analyse E. COLI cytochrome BO3 in msp nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N9Z
- Type
- protein
- Length
- 1,202 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
- LHG, 3PE, UQ8, HEO, HEM, CDL, CU, ZN
- Pockets
- 14 · best druggability 0.91
Structure
electron microscopy · 4 distinct chains · 66% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Cytochrome O ubiquinol oxidase, subunit I (EC 1.10.3.-) | protein | 658 | 71% helix, 2% strand | H4KCU1 |
| G | Ubiquinol oxidase subunit 2 | protein | 262 | 35% helix, 24% strand | A0A024L5V9 |
| H | Cytochrome O ubiquinol oxidase | protein | 184 | 87% helix, 0% strand | D6I7E4 |
| I | Cytochrome O ubiquinol oxidase, subunit IV (EC 1.10.3.-) | protein | 98 | 83% helix, 0% strand | I2RK84 |
Ligands and binding sites
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 9 copies · chains F, H, I
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains F, H
- UQ8 · Ubiquinone-8 · ligand · chains F
- HEO · Heme O · ligand · chains F, G
- HEM · Protoporphyrin IX containing Fe · ligand · chains F
- CDL · Cardiolipin · ligand · chains F, G, I
- CU · Copper (II) ion · metal · chains F
- ZN · Zinc ion · metal · chains F, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.91 | 0.93 | 99 | HEO, HEM |
| 2 | 1113 | 0.84 | 0.84 | 75 | 3PE |
| 3 | 440 | 0.70 | 0.81 | 61 | empty |
| 4 | 419 | 0.67 | 0.79 | 42 | empty |
| 5 | 186 | 0.64 | 0.84 | 24 | empty |
Interfaces
5 interfaces between chains.
- F–G · 3792 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 1762 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 1339 Ų buried · 9 hydrogen bonds · protein-protein
- F–I · 931 Ų buried · 6 hydrogen bonds · protein-protein
- G–I · 324 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7N9Z · E. coli cytochrome bo3 in MSP nanodisc · the same entry in another collection · chain F against F, 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 7N9Z · PDBe 7N9Z · UniProt H4KCU1 · UniProt A0A024L5V9 · UniProt D6I7E4 · UniProt I2RK84
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