MolNFT v1 · #109394 · protein

OPSIN/G(ALPHA) peptide complex stabilized by nonyl-glucoside

4X1H · Rhodopsin: “OPSIN/G(ALPHA) peptide complex stabilized by nonyl-glucoside”. X-ray diffraction, 4 ligands (BNG, PLM, NAG), 4 pockets (best druggability 0.84). MolNFT v1 #109394 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4X1H
Type: protein
Length: 337 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin; C-terminal derived peptide of guanine nucleotide-binding protein G(T) subunit…
UniProt: P02699
Ligands: BNG, PLM, NAG, BMA
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	326	70% helix, 4% strand	P02699
C	C-terminal derived peptide of guanine nucleotide-binding protein G(T) subunit alpha-1	protein	11	55% helix, 0% strand	—

Ligands and binding sites

BNG · nonyl beta-D-glucopyranoside · ligand · 2 copies · chains A
PLM · Palmitic acid · ligand · 2 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
BMA · beta-D-mannopyranose · sugar · 2 copies

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	269	0.84	0.95	39	BNG
2	86	0.47	0.81	25	empty
3	111	0.44	0.77	15	empty
4	64	0.32	0.75	11	empty

Interfaces

1 interface between chains.

A–C · 650 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 glycan, 2 lipid, 1 disulfide (N-glycosylation, palmitoylation, disulfide).

Compared structures

4X1H · Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside · the same entry in another collection · chain A against A, TM-score 1.00
P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P02699
Elsewhere: RCSB PDB 4X1H · PDBe 4X1H · UniProt P02699

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