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Crystal structure of G protein-coupled receptor kinase 2 in complex with galpha-Q and gbetagamma subunits

Analyse Crystal structure of G protein-coupled receptor kinase 2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BCJ
Type: protein
Length: 1,344 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: G-protein-coupled receptor kinase 2; Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
EC: 2.7.11.15
UniProt: P21146, P62871, P63212, P10824, P21279
Ligands: ACE, ALF, GDP, MG
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	G-protein-coupled receptor kinase 2 (EC 2.7.11.15)	protein	624	45% helix, 15% strand	P21146
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	7% helix, 47% strand	P62871
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	64	53% helix, 0% strand	P63212
Q	Guanine nucleotide-binding protein G(I) subunit alpha-1, guanine nucleotide-binding protein G(Q) subunit alpha chimera	protein	317	49% helix, 13% strand	P10824, P21279

Ligands and binding sites

ACE · Acetyl group · ligand · chains B
ALF · Tetrafluoroaluminate ion · ligand · chains Q
GDP · Guanosine-5'-diphosphate · ligand · chains Q
MG · Magnesium ion · metal · chains Q

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	606	0.79	0.84	58	empty
2	199	0.71	0.88	37	MG, ALF, GDP
3	241	0.63	0.82	37	empty
4	416	0.61	0.76	51	empty
5	102	0.61	0.88	21	empty

Interfaces

3 interfaces between chains.

B–G · 2292 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1113 Å² buried · 19 hydrogen bonds · protein-protein
A–Q · 853 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2BCJ · Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and… · the same entry in another collection · chain A against A, TM-score 1.00
P21146 · AlphaFold monomer V2.0 prediction for beta-adrenergic receptor kinase 1 (P21146) · a predicted model of the same protein · chain A against A, TM-score 0.99
P62871 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
P21279 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(Q) subunit… · a predicted model of the same protein · chain Q against A, TM-score 0.99
P10824 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain Q against A, TM-score 0.97
P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G 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 P21146
Every structure of UniProt P62871
Every structure of UniProt P63212
Every structure of UniProt P10824
Every structure of UniProt P21279
Elsewhere: RCSB PDB 2BCJ · PDBe 2BCJ · UniProt P21146 · UniProt P62871 · UniProt P63212 · UniProt P10824 · UniProt P21279

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