3KRX

Human GRK2 in complex with Gbetgamma subunits and balanol (co-crystal)

PDB DOI: https://doi.org/10.2210/pdb3KRX/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, Bos taurus
Expression System: Spodoptera frugiperda, unidentified baculovirus
Mutation(s): No

Deposited: 2009-11-19 Released: 2010-02-16
Deposition Author(s): Tesmer, J.J.G., Tesmer, V.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of human g protein-coupled receptor kinase 2 in complex with the kinase inhibitor balanol.

Tesmer, J.J., Tesmer, V.M., Lodowski, D.T., Steinhagen, H., Huber, J.

(2010) J Med Chem 53: 1867-1870

PubMed: 20128603 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm9017515
Primary Citation of Related Structures:
3CIK, 3KRW, 3KRX

PubMed Abstract:
G protein-coupled receptor kinase 2 (GRK2) is a pharmaceutical target for the treatment of cardiovascular diseases such as congestive heart failure, myocardial infarction, and hypertension. To better understand how nanomolar inhibition and selectivity for GRK2 might be achieved, we have determined crystal structures of human GRK2 in complex with Gbetagamma in the presence and absence of the AGC kinase inhibitor balanol. The selectivity of balanol among human GRKs is assessed.

Organizational Affiliation

Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA. johntesmer@umich.edu

Macromolecule Content

Total Structure Weight: 125.96 kDa
Atom Count: 8,204
Modelled Residue Count: 1,017
Deposited Residue Count: 1,102
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-adrenergic receptor kinase 1	A	688	Homo sapiens	Mutation(s): 0 Gene Names: ADRBK1, BARK, BARK1, GRK2 EC: 2.7.11.15
UniProt & NIH Common Fund Data Resources
Find proteins for P25098 (Homo sapiens) Explore P25098 Go to UniProtKB: P25098
PHAROS: P25098 GTEx: ENSG00000173020
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25098
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	Bos taurus	Mutation(s): 0 Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus) Explore P62871 Go to UniProtKB: P62871
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62871
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	74	Bos taurus	Mutation(s): 0 Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BA1 Query on BA1 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BALANOL C₂₈ H₂₆ N₂ O₁₀ XYUFCXJZFZPEJD-XMSQKQJNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMT Query on CMT	C [auth G]	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
BA1	PDBBind: 3KRX	IC50: 42 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.076	α = 90
b = 73.29	β = 114.51
c = 121.78	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Tesmer, J.J.G.

Tesmer, V.M.

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description