Research workbench
Crystal structure of the H80R variant of NQO1 bound to dicoumarol
Analyse Crystal structure of the H80R variant of NQO1 bound to dicoumarol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUQ
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase [quinone] 1
- EC
- 1.6.5.2
- UniProt
- P15559
- Ligands
- DTC, FAD
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 273 | 41% helix, 16% strand | P15559 |
Ligands and binding sites
- DTC · Bishydroxy[2h-1-benzopyran-2-one,1,2-benzopyrone] · ligand · 3 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 18 | empty |
| 2 | 600 | 0.78 | 0.84 | 47 | ACT, FAD, DTC |
| 3 | 593 | 0.77 | 0.82 | 49 | FAD, DTC, ACT |
| 4 | 67 | 0.28 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2762 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5FUQ · Crystal structure of the H80R variant of NQO1 bound to dicoumarol · the same entry in another collection · chain A against A, TM-score 1.00
- P15559 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase [quinone] 1 (P15559) · 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 P15559
- Elsewhere: RCSB PDB 5FUQ · PDBe 5FUQ · UniProt P15559
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