Research workbench
Crystal structure of a complex of human NAD[P]H-quinone oxidoreductase and a chemotherapeutic drug (E09) at 2.5 a resolution
Analyse Crystal structure of a complex of human NAD[P]H-quinone oxidoreductase and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GG5
- Type
- protein
- Length
- 1,092 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, E09
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.99.2) | protein | 273 | 40% helix, 16% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
- E09 · 3-hydroxymethyl-5-aziridinyl-1methyl-2-[1H-indole-4,7-dione]-propanol · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.78 | 0.84 | 48 | E09, FAD |
| 2 | 95 | 0.78 | 0.98 | 18 | empty |
| 3 | 582 | 0.78 | 0.84 | 47 | E09, FAD |
| 4 | 93 | 0.78 | 0.98 | 19 | empty |
| 5 | 601 | 0.77 | 0.83 | 48 | FAD, E09 |
Interfaces
2 interfaces between chains.
- A–C · 2702 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2693 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1GG5 · Crystal structure of a complex of human NAD[P]H-quinone oxidoreductase and a… · 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 1GG5 · PDBe 1GG5 · UniProt P15559
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