MolNFT v1 · #113078 · protein
Crystal structure of the R139W variant of human NAD(P)H:QUINONE oxidoreductase
5A4K · NAD(P)H dehydrogenase [quinone] 1: “Crystal structure of the R139W variant of human NAD(P)H:QUINONE oxidoreductase”. X-ray diffraction, 1 ligand (FAD), 11 pockets (best druggability 0.86). MolNFT v1 #113078 on GenesisL1: 3D…
- PDB
- 5A4K
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase [quinone] 1
- EC
- 1.6.5.2
- UniProt
- P15559
- Ligands
- FAD
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 271 | 38% helix, 16% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, D, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.86 | 0.87 | 107 | empty |
| 2 | 80 | 0.77 | 0.99 | 19 | empty |
| 3 | 90 | 0.77 | 0.98 | 18 | empty |
| 4 | 605 | 0.76 | 0.82 | 50 | FAD |
| 5 | 569 | 0.76 | 0.83 | 47 | FAD |
Interfaces
5 interfaces between chains.
- A–D · 2834 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2808 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 369 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 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 5A4K · PDBe 5A4K · UniProt P15559
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