MolNFT v1 · #110338 · protein

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9

4XTN · Sodium pumping rhodopsin: “Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9”. X-ray diffraction, 3 ligands (LFA, MPG, NA), 20 pockets (best druggability 0.75). MolNFT v1 #110338 on GenesisL1…

PDB: 4XTN
Type: protein
Length: 2,715 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium pumping rhodopsin
UniProt: N0DKS8
Ligands: LFA, MPG, NA
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 76% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Sodium pumping rhodopsin	protein	273	76% helix, 3% strand	N0DKS8
B	Sodium pumping rhodopsin	protein	270	76% helix, 3% strand	N0DKS8
C, F	Sodium pumping rhodopsin	protein	271	76% helix, 3% strand	N0DKS8
D, G, I	Sodium pumping rhodopsin	protein	271	76% helix, 3% strand	N0DKS8
E	Sodium pumping rhodopsin	protein	272	76% helix, 3% strand	N0DKS8
J	Sodium pumping rhodopsin	protein	272	76% helix, 3% strand	N0DKS8

Ligands and binding sites

LFA · Eicosane · ligand · 118 copies · chains A, E, B, C, D, F, G, J, H, I
MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.75	0.77	101	LFA
2	499	0.75	0.83	57	LFA
3	532	0.75	0.82	67	LFA
4	655	0.75	0.80	53	LFA
5	616	0.74	0.80	51	LFA

Interfaces

23 interfaces between chains.

I–J · 1391 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 1372 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1352 Å² buried · 8 hydrogen bonds · protein-protein
F–J · 1323 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 1322 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (nonstandard).

Compared structures

4XTN · Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9 · 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 4XTN · PDBe 4XTN · UniProt N0DKS8

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