MolNFT v1 · #154574 · protein

Crystal structure of thermophilic rhodopsin from rubrobacter xylanophilus

6KFQ: “Crystal structure of thermophilic rhodopsin from rubrobacter xylanophilus”. X-ray diffraction, 3 ligands (MPG, RET, SO4), 1 pocket (best druggability 0.78). MolNFT v1 #154574 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6KFQ
Type: protein
Length: 229 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: Q1AUE6
Ligands: MPG, RET, SO4
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 81% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	229	81% helix, 2% strand	Q1AUE6

Ligands and binding sites

MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 16 copies · chains A
RET · Retinal · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · 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	115	0.78	0.96	21	RET

Modifications

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

Compared structures

6KFQ · Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus · 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 Q1AUE6
Elsewhere: RCSB PDB 6KFQ · PDBe 6KFQ · UniProt Q1AUE6

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