Research workbench
Structure of trihydroxynaphthalene reductase in complex with NADPH and an active site inhibitor
Analyse Structure of trihydroxynaphthalene reductase in complex with NADPH and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YBV
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trihydroxynaphthalene reductase
- EC
- 1.3.1.50
- UniProt
- Q12634
- Ligands
- NDP, BEA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trihydroxynaphthalene reductase (EC 1.3.1.50) | protein | 270 | 50% helix, 15% strand | Q12634 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- BEA · 5-methyl-1,2,4-triazolo[3,4-b]benzothiazole · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.78 | 0.87 | 43 | NDP, BEA |
| 2 | 399 | 0.77 | 0.86 | 43 | NDP, BEA |
| 3 | 448 | 0.62 | 0.76 | 46 | empty |
| 4 | 85 | 0.38 | 0.77 | 15 | empty |
| 5 | 71 | 0.37 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2062 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1YBV · Structure of trihydroxynaphthalene reductase in complex with NADPH and an active site… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12634 · AlphaFold monomer V2.0 prediction for tetrahydroxynaphthalene reductase (Q12634) · 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 Q12634
- Elsewhere: RCSB PDB 1YBV · PDBe 1YBV · UniProt Q12634
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