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Crystal structure of human dt-diaphorase (NAD(P)H oxidoreductase)
Analyse Crystal structure of human dt-diaphorase (NAD(P)H oxidoreductase) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QBG
- Type
- protein
- Length
- 1,087 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase [quinone] 1
- EC
- 1.6.99.2
- UniProt
- P15559
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.99.2) | protein | 272 | 38% helix, 15% strand | P15559 |
| B | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.99.2) | protein | 271 | 38% helix, 15% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.84 | 0.85 | 98 | empty |
| 2 | 116 | 0.79 | 0.98 | 21 | empty |
| 3 | 115 | 0.79 | 0.97 | 20 | empty |
| 4 | 604 | 0.76 | 0.82 | 49 | FAD |
| 5 | 561 | 0.76 | 0.82 | 45 | FAD |
Interfaces
5 interfaces between chains.
- A–B · 2852 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2803 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1QBG · Crystal structure of human dt-diaphorase (NAD(P)H oxidoreductase) · 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 B 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 1QBG · PDBe 1QBG · UniProt P15559
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