MolNFT v1 · #168921 · protein
Takifugu rubripes vkor-like C138S mutant with vitamin K1
6WV8 · Vitamin K epoxide reductase-like protein, termini…: “Takifugu rubripes vkor-like C138S mutant with vitamin K1”. X-ray diffraction, 2 ligands (CRO, PQN), 3 pockets (best druggability 0.78). MolNFT v1 #168921 on GenesisL1: 3D…
- PDB
- 6WV8
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein
- UniProt
- K0NYR4, Q6TEK8, A0A059PIQ0
- Ligands
- CRO, PQN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein | protein | 394 | 32% helix, 31% strand | K0NYR4, Q6TEK8, A0A059PIQ0 |
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 · chains A
- PQN · Phylloquinone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.78 | 0.96 | 25 | CRO |
| 2 | 333 | 0.75 | 0.86 | 36 | PQN |
| 3 | 323 | 0.60 | 0.78 | 39 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 6WV8 · Takifugu rubripes VKOR-like C138S mutant with vitamin K1 · the same entry in another collection · chain A against A, 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 K0NYR4
- Every structure of UniProt Q6TEK8
- Every structure of UniProt A0A059PIQ0
- Elsewhere: RCSB PDB 6WV8 · PDBe 6WV8 · UniProt K0NYR4 · UniProt Q6TEK8 · UniProt A0A059PIQ0
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