4MK0: G protein-coupled receptor kinase 2

Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative. Determined by X-ray diffraction at 2.4 Å resolution. Released 22 Jan 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Bos taurus
Chains: 3
Atoms: 8,408
Mol. weight: 118.78 kDa
Ligands: 29X
Released: 22 Jan 2014

Explore 4MK0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MK0 contains 43 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: 35 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	115-119	5
α-helix	126-136	11
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	215-223	9	1
α-helix	224-230	7
α-helix	233-246	14
β-strand	254	1	2
β-strand	257-263	7	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
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	393-395	3
α-helix	399-407	9
α-helix	410-412	3
α-helix	419-428	10
α-helix	444-448	5
α-helix	451-453	3
α-helix	458-462	5
α-helix	467-468	2
β-strand	481	1	1
α-helix	500-503	4
α-helix	504-506	3
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	576-584	9	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	637-658	22

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	47-51	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	120-125	6	7
β-strand	134-140	7	7
β-strand	146-153	8	8
β-strand	156-161	6	8
β-strand	165-170	6	8
β-strand	175-181	7	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	207-212	6	9
β-strand	217-223	7	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	336-339	4	5

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-adrenergic receptor kinase 1	A	protein	640	Homo sapiens	P25098 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	59	Bos taurus	P63212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4MK0_1 Beta-adrenergic receptor kinase 1 (chains A)
KKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEI
KKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPY
IEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCR
KADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSF
ILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHG
HVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHS
PFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKE
SPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNF
PLTISERWQQEVAETVFDTINAETDRLEARKKAKNKQLGHEEDYALGKDCIMHGYMSKMG
NPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQ
FILQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPA

Sequence of entity 2 (B), FASTA

>4MK0_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>4MK0_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
TASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Ligands and cofactors

ID	Name	Formula	Copies
29X	5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-1H-isoindol-1-one	C20 H19 F N2 O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog. Homan, K.T., Wu, E., Wilson, M.W. et al. Mol Pharmacol (2014) 85:237-248. DOI 10.1124/mol.113.089631 · 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)
5WG4 2.31 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257284
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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