5UKK: Human GRK2

Human GRK2 in complex with human G-beta-gamma subunits and CCG211998 (14ak). Determined by X-ray diffraction at 2.6 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,161
Mol. weight: 118.92 kDa
Ligands: MG, 8DJ
Released: 5 Apr 2017

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

Secondary structure: helices and β-sheets

5UKK contains 38 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: 32 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	39-48	10
α-helix	55-59	5
α-helix	62-74	13
α-helix	80-94	15
α-helix	98-109	12
α-helix	127-137	11
α-helix	143-145	3
α-helix	147-157	11
α-helix	160-167	8
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	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	346-347	2
α-helix	359-362	4
α-helix	371-386	16
α-helix	393-395	3
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	471-473	3
β-strand	481	1	1
α-helix	502-506	5
β-strand	511-512	2	1
α-helix	514-523	10
α-helix	526-547	22
β-strand	561-568	8	4
β-strand	576-583	8	4
β-strand	587-591	5	4
β-strand	599-602	4	4
β-strand	606-614	9	4
β-strand	617-624	8	4
β-strand	628-633	6	4
α-helix	637-659	23

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
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	88-94	7	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	165-170	6	8
β-strand	175-181	7	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	249-254	6	10
β-strand	259-264	6	10
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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-44	15
α-helix	45-47	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-adrenergic receptor kinase 1	A	protein	642	Homo sapiens	P25098 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	57	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5UKK_1 Beta-adrenergic receptor kinase 1 (chains A)
KKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEI
KKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPY
IEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCR
KADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSF
ILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHG
HVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHS
PFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKE
SPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNF
PLTISERWQQEVAETVFDTINAETDRLEARKKAKNKQLGHEEDYALGKDCIMHGYMSKMG
NPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQ
FILQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRAP

Sequence of entity 2 (B), FASTA

>5UKK_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

>5UKK_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
8DJ	5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[…	C26 H26 F N3 O4	1

Primary citation

Structure-Based Design of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors Based on Paroxetine. Waldschmidt, H.V., Homan, K.T., Cato, M.C. et al. J Med Chem (2017) 60:3052-3069. DOI 10.1021/acs.jmedchem.7b00112 · 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
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
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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