MolNFT v1 · #149356 · protein
Structure of human NAD(P) H:QUINONE oxidoreductase in complex with N- (2-BROMOPHENYL)PYRROLIDINE-1-sulfonamide
6FY4 · NAD(P)H dehydrogenase [quinone] 1: “Structure of human NAD(P) H:QUINONE oxidoreductase in complex with N- (2-BROMOPHENYL)PYRROLIDINE-1-sulfonamide”. X-ray diffraction, 2 ligands (FAD, EAW), 9 pockets (best druggability 0.86). MolNFT…
- PDB
- 6FY4
- Type
- protein
- Length
- 1,080 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, EAW
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% 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 | 270 | 39% helix, 16% strand | P15559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- EAW · N-(2-bromophenyl)pyrrolidine-1-sulfonamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.86 | 0.87 | 108 | empty |
| 2 | 766 | 0.77 | 0.81 | 51 | EAW, FAD |
| 3 | 554 | 0.77 | 0.83 | 51 | FAD |
| 4 | 70 | 0.75 | 0.99 | 18 | empty |
| 5 | 547 | 0.75 | 0.82 | 51 | FAD |
Interfaces
5 interfaces between chains.
- C–D · 2805 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2716 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 493 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FY4 · Structure of human NAD(P) H:qui oxidoreductase in complex with… · 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 6FY4 · PDBe 6FY4 · UniProt P15559
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