MolNFT v1 · #168920 · protein
Human vkor with chlorophacinone
6WV7 · Vitamin K epoxide reductase, termini restrained by green…: “Human vkor with chlorophacinone”. X-ray diffraction, 2 ligands (CRO, UAJ), 6 pockets (best druggability 0.79). MolNFT v1 #168920 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WV7
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin K epoxide reductase, termini restrained by green fluorescent protein
- EC
- 1.17.4.4
- UniProt
- A0A059PIQ0, Q9BQB6
- Ligands
- CRO, UAJ
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin K epoxide reductase, termini restrained by green fluorescent protein (EC 1.17.4.4) | protein | 380 | 35% helix, 32% strand | A0A059PIQ0, Q9BQB6 |
| B | Vitamin K epoxide reductase, termini restrained by green fluorescent protein (EC 1.17.4.4) | protein | 388 | 36% helix, 31% strand | A0A059PIQ0, Q9BQB6 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- UAJ · Chlorophacinone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.79 | 0.82 | 73 | CRO |
| 2 | 650 | 0.78 | 0.84 | 67 | CRO |
| 3 | 292 | 0.77 | 0.89 | 38 | UAJ |
| 4 | 292 | 0.76 | 0.88 | 38 | UAJ |
| 5 | 64 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 disulfide (chromophore, disulfide).
Compared structures
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 A0A059PIQ0
- Every structure of UniProt Q9BQB6
- Elsewhere: RCSB PDB 6WV7 · PDBe 6WV7 · UniProt A0A059PIQ0 · UniProt Q9BQB6
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