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Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside
Analyse Crystal structure of active conformation of GPCR opsin stabilized by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J4Q
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin; Guanine nucleotide-binding protein G(T) subunit alpha-1
- UniProt
- P02699, P04695
- Ligands
- PLM, NAG, GLC, BMA, MAN, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 69% helix, 4% strand | P02699 |
| B | Guanine nucleotide-binding protein G(T) subunit alpha-1 | protein | 11 | 55% helix, 0% strand | P04695 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A
- ACT · Acetate ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.83 | 0.94 | 36 | BOG, ACT |
| 2 | 105 | 0.52 | 0.82 | 20 | empty |
| 3 | 75 | 0.45 | 0.82 | 25 | empty |
| 4 | 56 | 0.44 | 0.84 | 15 | empty |
| 5 | 50 | 0.29 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).
Compared structures
- 4J4Q · Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside · 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
- P04695 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.67
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
- Every structure of UniProt P04695
- Elsewhere: RCSB PDB 4J4Q · PDBe 4J4Q · UniProt P02699 · UniProt P04695
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