Research workbench
Takifugu rubripes vkor-like with vitamin K1 epoxide at non-catalytic state
Analyse Takifugu rubripes vkor-like with vitamin K1 epoxide at non-catalytic state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVA
- Type
- protein
- Length
- 411 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
- EC
- 1.17.4.4
- UniProt
- P42212, Q6TEK8
- Ligands
- CRO
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein (EC 1.17.4.4) | protein | 411 | 34% helix, 29% strand | P42212, Q6TEK8 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.77 | 0.97 | 29 | CRO |
| 2 | 292 | 0.76 | 0.88 | 35 | empty |
| 3 | 268 | 0.66 | 0.83 | 41 | empty |
| 4 | 127 | 0.42 | 0.76 | 24 | empty |
| 5 | 77 | 0.38 | 0.78 | 23 | empty |
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (chromophore, disulfide).
Compared structures
- 6WVA · Takifugu rubripes VKOR-like with vitamin K1 epoxide at non-catalytic state · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.55
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 P42212
- Every structure of UniProt Q6TEK8
- Elsewhere: RCSB PDB 6WVA · PDBe 6WVA · UniProt P42212 · UniProt Q6TEK8
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