MolNFT v1 · #170579 · protein

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0

6YBZ · Sodium pumping rhodopsin: “Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0”. X-ray diffraction, 3 ligands (LFA, RET, NA), 13 pockets (best druggability 0.74). MolNFT v1…

PDB: 6YBZ
Type: protein
Length: 1,347 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium pumping rhodopsin
UniProt: N0DKS8
Ligands: LFA, RET, NA
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Sodium pumping rhodopsin	protein	269	77% helix, 3% strand	N0DKS8
D	Sodium pumping rhodopsin	protein	271	76% helix, 3% strand	N0DKS8

Ligands and binding sites

LFA · Eicosane · ligand · 19 copies · chains A, B, E, C, D
RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B, C, D, E
BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B, C, D, E

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

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1046	0.74	0.76	85	LFA
2	133	0.74	0.92	24	LFA, RET
3	134	0.73	0.92	25	LFA, RET
4	130	0.73	0.92	26	LFA, RET
5	136	0.72	0.91	24	LFA, RET

Interfaces

5 interfaces between chains.

C–D · 1281 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 1264 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 1256 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 1249 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1234 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 cofactor (retinal Schiff base).

Compared structures

6YBZ · 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 6YBZ · PDBe 6YBZ · UniProt N0DKS8

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