3V5W: Human G Protein-Coupled Receptor Kinase 2

Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits and Paroxetine. Determined by X-ray diffraction at 2.07 Å resolution. Released 26 Sept 2012.

Method: X-ray diffraction
Resolution: 2.07 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 8,485
Mol. weight: 126.14 kDa
Ligands: MG, 8PR
Released: 26 Sept 2012

Explore 3V5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V5W contains 46 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: 37 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	39-49	11
α-helix	55-59	5
α-helix	62-75	14
α-helix	77-79	3
α-helix	80-93	14
α-helix	98-109	12
α-helix	112-118	7
α-helix	126-137	12
α-helix	147-157	11
α-helix	160-167	8
α-helix	169-181	13
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	224-229	6
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	288-290	3
α-helix	291-309	19
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	354-356	3
α-helix	359-362	4
α-helix	371-386	16
α-helix	393-395	3
α-helix	399-408	10
α-helix	409-411	3
α-helix	419-428	10
α-helix	433-435	3
α-helix	444-447	4
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	500-503	4
β-strand	511-512	2	1
α-helix	514-522	9
α-helix	526-546	21
β-strand	561-567	7	4
β-strand	577-584	8	4
β-strand	587-591	5	4
β-strand	599-602	4	4
α-helix	603-605	3
β-strand	606-613	8	4
β-strand	618-624	7	4
β-strand	628-633	6	4
α-helix	637-658	22

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	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	121-125	5	7
β-strand	134-139	6	7
β-strand	146-153	8	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	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G-protein coupled receptor kinase 2	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	77	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3V5W_1 G-protein coupled receptor kinase 2 (chains A)
MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFS
QKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLAC
SHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNV
ELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNER
IMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAE
IILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPE
VLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPE
LRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAA
DAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARK
KAKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSL
LTMEEIQSVEETQIKERKCLLLKIRGGKQFILQCDSDPELVQWKKELRDAYREAQQLVQR
VPKMKNKPRSPVVELSKVPLVQRGSANGL

Sequence of entity 2 (B), FASTA

>3V5W_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

>3V5W_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
HHHHHHMASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPV
PASENPFREKKFFSAIL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
8PR	Paroxetine	C19 H20 F N O3	1

Primary citation

Paroxetine is a direct inhibitor of g protein-coupled receptor kinase 2 and increases myocardial contractility. Thal, D.M., Homan, K.T., Chen, J. et al. ACS Chem Biol (2012) 7:1830-1839. DOI 10.1021/cb3003013 · PubMed

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

5UKL 2.15 Å, Human GRK2 in complex with Gbetagamma subunits and CCG222886 (14bd)
5WG4 2.31 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257284
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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