MolNFT v1 · #87911 · protein
Crystal structure of the complex of the P187S variant of human NAD(P) H:QUINONE oxidoreductase with cibacron blue at 2.7 a resolution
4CF6 · NAD(P)H dehydrogenase [quinone] 1: “Crystal structure of the complex of the P187S variant of human NAD(P) H:QUINONE oxidoreductase with cibacron…”. X-ray diffraction, 2 ligands (FAD, CBD), 4 pockets (best druggability 0.78). MolNFT…
- PDB
- 4CF6
- Type
- protein
- Length
- 541 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
- FAD, CBD
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 270 | 34% helix, 15% strand | P15559 |
| B | NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2) | protein | 271 | 35% helix, 15% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CBD · Cibacron blue · ligand · 2 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 | 94 | 0.78 | 0.98 | 20 | empty |
| 2 | 617 | 0.77 | 0.83 | 50 | FAD, CBD |
| 3 | 615 | 0.76 | 0.82 | 51 | FAD, CBD |
| 4 | 57 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2732 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4CF6 · Crystal structure of the complex of the P187S variant of human NAD(P) H:qui… · 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 4CF6 · PDBe 4CF6 · UniProt P15559
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