Research workbench
OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation
Analyse OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K8E
- Type
- protein
- Length
- 399 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH dehydrogenase 1
- EC
- 1.6.99.1
- UniProt
- Q02899
- Ligands
- FMN, 0WV, NA, MG, CL
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 399 | 39% helix, 13% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- 0WV · 2-methyl-5-(prop-1-en-2-yl)phenol · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PGE · Triethylene glycol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.83 | 0.94 | 43 | FMN, 0WV, CL |
Compared structures
- 4K8E · OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation · the same entry in another collection · chain A against A, TM-score 1.00
- Q02899 · AlphaFold monomer V2.0 prediction for NADPH dehydrogenase 1 (Q02899) · a predicted model of the same protein · 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 Q02899
- Elsewhere: RCSB PDB 4K8E · PDBe 4K8E · UniProt Q02899
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