MolNFT v1 · #105862 · protein
Crystal structure of human COQ9 in complex with a phospholipid, northeast structural genomics consortium target HR5043
4RHP · Ubiquinone biosynthesis protein COQ9, mitochondrial: “Crystal structure of human COQ9 in complex with a phospholipid, northeast structural genomics consortium…”. X-ray diffraction, 1 ligand (PEF), 2 pockets (best druggability 0.86).…
- PDB
- 4RHP
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinone biosynthesis protein COQ9, mitochondrial
- UniProt
- O75208
- Ligands
- PEF
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinone biosynthesis protein COQ9, mitochondrial | protein | 189 | 77% helix, 0% strand | O75208 |
| B | Ubiquinone biosynthesis protein COQ9, mitochondrial | protein | 207 | 75% helix, 0% strand | O75208 |
Ligands and binding sites
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.86 | 0.88 | 67 | PEF |
| 2 | 50 | 0.36 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 4RHP · Crystal structure of human COQ9 in complex with a phospholipid, Northeast Structural… · the same entry in another collection · chain A against A, TM-score 1.00
- O75208 · AlphaFold monomer V2.0 prediction for ubiquinone biosynthesis protein COQ9, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O75208
- Elsewhere: RCSB PDB 4RHP · PDBe 4RHP · UniProt O75208
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