Research workbench
Structure of trihydroxynaphthalene reductase in complex with NADPH and 4-nitro-inden-1-one
Analyse Structure of trihydroxynaphthalene reductase in complex with NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DOH
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trihydroxynaphthalene reductase
- EC
- 1.1.1.252
- UniProt
- Q12634
- Ligands
- NDP, NID
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trihydroxynaphthalene reductase (EC 1.1.1.252) | protein | 273 | 51% helix, 15% strand | Q12634 |
| B | Trihydroxynaphthalene reductase (EC 1.1.1.252) | protein | 271 | 50% helix, 14% strand | Q12634 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- NID · 4-nitro-inden-1-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.77 | 0.87 | 44 | NDP, NID |
| 2 | 376 | 0.76 | 0.86 | 43 | NDP, NID |
| 3 | 415 | 0.62 | 0.77 | 45 | empty |
| 4 | 159 | 0.45 | 0.76 | 32 | empty |
| 5 | 63 | 0.35 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2352 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1DOH · Structure of trihydroxynaphthalene reductase in complex with NADPH and 4-nitro-inden-1-one · 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 B 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 1DOH · PDBe 1DOH · UniProt Q12634
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