MolNFT v1 · #86717 · protein

Night blindness causing G90D rhodopsin in the active conformation

4BEZ: “Night blindness causing G90D rhodopsin in the active conformation”. X-ray diffraction, 6 ligands (ACE, PLM, NAG), 5 pockets (best druggability 0.83). MolNFT v1 #86717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BEZ
Type: protein
Length: 326 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P02699
Ligands: ACE, PLM, NAG, BMA, MAN, SO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	326	71% helix, 4% strand	P02699

Ligands and binding sites

ACE · Acetyl group · ligand · chains A
PLM · Palmitic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · chains A
ACT · Acetate ion · additive · chains A
BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	264	0.83	0.94	43	ACT
2	122	0.53	0.82	21	empty
3	228	0.53	0.76	23	empty
4	60	0.52	0.86	16	empty
5	55	0.30	0.75	12	empty

Modifications

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

Compared structures

4BEZ · Night blindness causing G90D rhodopsin in the active conformation · 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 4BEZ · PDBe 4BEZ · UniProt P02699

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