MolNFT v1 · #170578 · protein

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6

6YBY · Sodium pumping rhodopsin: “Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6”. X-ray diffraction, 3 ligands (LFA, RET, NA), 1 pocket (best druggability 0.72). MolNFT v1 #170578…

PDB: 6YBY
Type: protein
Length: 270 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium pumping rhodopsin
UniProt: N0DKS8
Ligands: LFA, RET, NA
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sodium pumping rhodopsin	protein	270	76% helix, 3% strand	N0DKS8

Ligands and binding sites

LFA · Eicosane · ligand · 34 copies · chains A
RET · Retinal · ligand · chains A
NA · Sodium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.72	0.91	25	LFA, RET

Modifications

Observed in the structure: 1 cofactor (retinal Schiff base).

Compared structures

6YBY · Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the… · the same entry in another collection · 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 N0DKS8
Elsewhere: RCSB PDB 6YBY · PDBe 6YBY · UniProt N0DKS8

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