MolNFT v1 · #185661 · protein

Structure of wrba from salmonella typhimurium bound to ME0052

7Q6N · NAD(P)H dehydrogenase (quinone): “Structure of wrba from salmonella typhimurium bound to ME0052”. X-ray diffraction, 2 ligands (8YX, FMN), 8 pockets (best druggability 0.81). MolNFT v1 #185661 on GenesisL1: 3D structure, binding…

PDB: 7Q6N
Type: protein
Length: 797 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase (quinone)
EC: 1.6.5.2
UniProt: Q8ZQ40
Ligands: 8YX, FMN
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2)	protein	197	38% helix, 21% strand	Q8ZQ40
B, C	NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2)	protein	198	38% helix, 21% strand	Q8ZQ40
D	NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2)	protein	204	37% helix, 20% strand	Q8ZQ40

Ligands and binding sites

8YX · 2-azanyl-4,6-bis(bromanyl)phenol · ligand · 4 copies · chains A, B, D, C
FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, D, B
PG4 · Tetraethylene glycol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	181	0.81	0.96	36	empty
2	143	0.80	0.97	31	empty
3	98	0.77	0.98	24	empty
4	453	0.67	0.79	42	8YX, FMN
5	472	0.67	0.79	41	FMN, 8YX

Interfaces

6 interfaces between chains.

A–B · 1072 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1028 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 873 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 869 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 726 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7Q6N · Structure of WrbA from Salmonella Typhimurium bound to ME0052 · the same entry in another collection · chain A against A, TM-score 1.00
Q8ZQ40 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase (quinone) (Q8ZQ40) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q8ZQ40
Elsewhere: RCSB PDB 7Q6N · PDBe 7Q6N · UniProt Q8ZQ40

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