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Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form

Analyse Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RF0
Type: protein
Length: 1,370 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: 16 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 75% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sodium pumping rhodopsin	protein	273	76% helix, 3% strand	N0DKS8
B, E	Sodium pumping rhodopsin	protein	274	76% helix, 3% strand	N0DKS8
C	Sodium pumping rhodopsin	protein	275	75% helix, 3% strand	N0DKS8
D	Sodium pumping rhodopsin	protein	274	75% helix, 3% strand	N0DKS8

Ligands and binding sites

LFA · Eicosane · ligand · 10 copies · chains A, B, C, D, E
RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 5 copies · chains A, B, E, C, D
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · 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

16 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	137	0.75	0.93	26	RET
2	141	0.74	0.92	26	RET
3	143	0.74	0.92	26	RET
4	147	0.73	0.91	24	RET
5	145	0.73	0.91	26	RET

Interfaces

5 interfaces between chains.

D–E · 1521 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1500 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1472 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 1458 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 1431 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6RF0 · Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form · 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 6RF0 · PDBe 6RF0 · UniProt N0DKS8

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