MolNFT v1 · #37647 · protein

Crystallographic model of bathorhodopsin

2G87: “Crystallographic model of bathorhodopsin”. X-ray diffraction, 9 ligands (PLM, ACE, RET), 10 pockets (best druggability 0.82). MolNFT v1 #37647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2G87
Type: protein
Length: 696 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P02699
Ligands: PLM, ACE, RET, HTO, NAG, BMA, MAN, ZN, HG
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Rhodopsin	protein	348	61% helix, 3% strand	P02699

Ligands and binding sites

PLM · Palmitic acid · ligand · 6 copies · chains A, B
ACE · Acetyl group · ligand · 2 copies · chains A, B
RET · Retinal · ligand · 2 copies · chains A, B
HTO · Heptane-1,2,3-triol · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
MAN · alpha-D-mannopyranose · sugar
ZN · Zinc ion · metal · 7 copies · chains A, B
HG · Mercury (II) ion · metal · 6 copies · chains A, B
HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 4 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.82	0.97	29	RET
2	153	0.82	0.97	30	RET
3	819	0.70	0.75	65	HG, PLM, HTG
4	444	0.62	0.75	43	PLM, HTO, HTG
5	228	0.61	0.80	28	ZN, PLM

Interfaces

1 interface between chains.

A–B · 792 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 4 lipid, 2 cofactor, 2 covalent, 2 disulfide (N-glycosylation, palmitoylation, retinal Schiff base, covalent ligand, disulfide).

Compared structures

2G87 · Crystallographic model of bathorhodopsin · 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 0.87

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 2G87 · PDBe 2G87 · UniProt P02699

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