Research workbench

NADH:QUINONE oxidoreductase (ndh-II) from staphylococcus aureus - E172S mutant

Analyse NADH:QUINONE oxidoreductase (ndh-II) from staphylococcus aureus - E172S mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NA4
Type: protein
Length: 398 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH dehydrogenase-like protein SAOUHSC_00878
EC: 1.6.99.-
UniProt: Q2FZV7
Ligands: FAD
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NADH dehydrogenase-like protein SAOUHSC_00878 (EC 1.6.99.-)	protein	398	36% helix, 28% strand	Q2FZV7

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1018	0.81	0.82	103	FAD
2	70	0.44	0.82	18	empty

Compared structures

5NA4 · NADH:qui oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q2FZV7 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase-like protein SAOUHSC_00878… · 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 Q2FZV7
Elsewhere: RCSB PDB 5NA4 · PDBe 5NA4 · UniProt Q2FZV7

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