MolNFT v1 · #101563 · protein
C50A mutant of synechococcus vkor, C2 crystal form (dehydrated)
4NV5 · VKORC1/THIOREDOXIN domain protein: “C50A mutant of synechococcus vkor, C2 crystal form (dehydrated)”. X-ray diffraction, 1 ligand (U10), 5 pockets (best druggability 0.78). MolNFT v1 #101563 on GenesisL1: 3D structure, binding sites…
- PDB
- 4NV5
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VKORC1/THIOREDOXIN domain protein
- UniProt
- Q2JJF6
- Ligands
- U10
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VKORC1/THIOREDOXIN domain protein | protein | 259 | 62% helix, 7% strand | Q2JJF6 |
| B | VKORC1/THIOREDOXIN domain protein | protein | 262 | 62% helix, 7% strand | Q2JJF6 |
Ligands and binding sites
- U10 · Ubiquinone-10 · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.78 | 0.90 | 38 | U10 |
| 2 | 305 | 0.75 | 0.87 | 45 | U10 |
| 3 | 212 | 0.53 | 0.77 | 25 | empty |
| 4 | 155 | 0.51 | 0.79 | 22 | empty |
| 5 | 136 | 0.51 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 450 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NV5 · C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated) · the same entry in another collection · chain A against A, TM-score 1.00
- Q2JJF6 · AlphaFold monomer V2.0 prediction for vitamin K epoxide reductase homolog (Q2JJF6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q2JJF6
- Elsewhere: RCSB PDB 4NV5 · PDBe 4NV5 · UniProt Q2JJF6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.