Research workbench
Takifugu rubripes vkor-like with warfarin
Analyse Takifugu rubripes vkor-like with warfarin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVB
- Type
- protein
- Length
- 408 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, SWF
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein | protein | 408 | 33% helix, 29% 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
- SWF · S-warfarin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.79 | 0.97 | 26 | CRO |
| 2 | 287 | 0.75 | 0.87 | 37 | SWF |
| 3 | 145 | 0.55 | 0.82 | 21 | empty |
| 4 | 86 | 0.39 | 0.78 | 16 | empty |
| 5 | 52 | 0.26 | 0.73 | 12 | empty |
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (chromophore, disulfide).
Compared structures
- 6WVB · Takifugu rubripes VKOR-like with warfarin · 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 6WVB · PDBe 6WVB · UniProt K0NYR4 · UniProt Q6TEK8 · UniProt A0A059PIQ0
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