MolNFT v1 · #158515 · protein

X-ray crystallographic structure of gloeobacter rhodopsin

6NWD · GLL0198 protein: “X-ray crystallographic structure of gloeobacter rhodopsin”. X-ray diffraction, 4 ligands (PX4, RET, D10), 2 pockets (best druggability 0.76). MolNFT v1 #158515 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6NWD
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GLL0198 protein
UniProt: Q7NP59
Ligands: PX4, RET, D10, D12
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 83% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GLL0198 protein	protein	246	83% helix, 4% strand	Q7NP59

Ligands and binding sites

PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A
RET · Retinal · ligand · chains A
D10 · Decane · ligand · chains A
D12 · Dodecane · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.76	0.93	26	RET
2	259	0.57	0.78	32	empty

Modifications

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

Compared structures

6NWD · X-ray Crystallographic structure of Gloeobacter rhodopsin · 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 Q7NP59
Elsewhere: RCSB PDB 6NWD · PDBe 6NWD · UniProt Q7NP59

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