5WG4: Human GRK2

Human GRK2 in complex with Gbetagamma subunits and CCG257284. Determined by X-ray diffraction at 2.31 Å resolution. Released 27 Dec 2017.

Method: X-ray diffraction
Resolution: 2.31 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 8,326
Mol. weight: 125.41 kDa
Ligands: AFV
Released: 27 Dec 2017

Explore 5WG4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WG4 contains 44 α-helices and 48 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 36 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	37-39	3
α-helix	40-48	9
α-helix	55-59	5
α-helix	62-74	13
α-helix	80-93	14
α-helix	98-108	11
α-helix	109-114	6
α-helix	115-118	4
α-helix	126-137	12
α-helix	147-156	10
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-182	14
α-helix	188-190	3
β-strand	191-199	9	1
β-strand	203-210	8	1
β-strand	216-223	8	1
α-helix	224-230	7
α-helix	233-246	14
β-strand	254	1	2
β-strand	257-262	6	1
β-strand	266-271	6	1
β-strand	278	1	2
α-helix	279-286	8
α-helix	289-290	2
α-helix	291-310	20
β-strand	313-314	2	3
α-helix	320-322	3
β-strand	323-325	3	2
β-strand	331-333	3	2
β-strand	340-341	2	3
α-helix	359-362	4
α-helix	371-386	16
α-helix	399-407	9
α-helix	419-428	10
α-helix	433-435	3
α-helix	444-448	5
α-helix	451-453	3
α-helix	458-462	5
α-helix	467-468	2
α-helix	472-473	2
β-strand	481	1	1
α-helix	500-504	5
β-strand	511-512	2	1
α-helix	514-522	9
α-helix	526-547	22
β-strand	561-568	8	4
α-helix	571-573	3
β-strand	576-583	8	4
β-strand	587-591	5	4
β-strand	599-602	4	4
β-strand	606-613	8	4
β-strand	618-624	7	4
β-strand	629-633	5	4
α-helix	637-659	23

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-52	6	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	89-94	6	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	120-125	6	7
β-strand	135-140	6	7
β-strand	146-151	6	8
β-strand	156-161	6	8
β-strand	166-170	5	8
β-strand	175-180	6	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	259-264	6	10
α-helix	272	1
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	293-298	6	11
β-strand	304-309	6	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	335-339	5	5

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-44	15
α-helix	53-55	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-adrenergic receptor kinase 1	A	protein	689	Homo sapiens	P25098 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5WG4_1 Beta-adrenergic receptor kinase 1 (chains A)
MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFS
QKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLAC
SHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNV
ELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNER
IMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAE
IILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPE
VLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPE
LRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAA
DAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARK
KAKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSL
LTMEEIQSVEETQIKERKCLLLKIRGGKQFILQCDSDPELVQWKKELRDAYREAQQLVQR
VPKMKNKPRSPVVELSKVPLVQRGSANGL

Sequence of entity 2 (B), FASTA

>5WG4_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>5WG4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Ligands and cofactors

ID	Name	Formula	Copies
AFV	2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(pyridin…	C26 H26 F N5 O2	1

Primary citation

Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors. Bouley, R., Waldschmidt, H.V., Cato, M.C. et al. Mol Pharmacol (2017) 92:707-717. DOI 10.1124/mol.117.110130 · PubMed

Other PDB entries of the same protein (UniProt P25098 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V5W 2.07 Å, Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits…
5UKL 2.15 Å, Human GRK2 in complex with Gbetagamma subunits and CCG222886 (14bd)
4MK0 2.4 Å, Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally…
6U7C 2.44 Å, Human GRK2 in complex with Gbetagamma subunits and CCG258747
7K7L 2.54 Å, Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the…
4PNK 2.56 Å, G protein-coupled receptor kinase 2 in complex with GSK180736A
5UKK 2.6 Å, Human GRK2 in complex with human G-beta-gamma subunits and CCG211998 (14ak)
7PWD 2.6 Å, Structure of an inhibited GRK2-G-beta and G-gamma complex
7K7Z 2.61 Å, Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the…
5UVC 2.65 Å, Design, Synthesis, and Evaluation of the First Selective and Potent G-protein-Coupled…
5UUU 2.7 Å, Design, Synthesis, and Evaluation of the First Selective and Potent G-protein-Coupled…
6C2Y 2.74 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257142

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