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- PDB-4wnk: Crystal Structure of Bovine G Protein Coupled-Receptor Kinase 5 i... -

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Basic information

Entry
Database: PDB / ID: 4wnk
TitleCrystal Structure of Bovine G Protein Coupled-Receptor Kinase 5 in Complex with CCG215022
ComponentsG protein-coupled receptor kinase 5
KeywordsLIGASE / G protein-coupled receptor kinase 5 / hydrolase / phosphorylation / cardiovascular disease
Function / homology
Function and homology information


G-protein-coupled receptor kinase / G protein-coupled receptor kinase activity / G alpha (s) signalling events / regulation of signal transduction / Wnt signaling pathway / protein autophosphorylation / protein kinase activity / protein serine/threonine kinase activity / lipid binding / negative regulation of apoptotic process ...G-protein-coupled receptor kinase / G protein-coupled receptor kinase activity / G alpha (s) signalling events / regulation of signal transduction / Wnt signaling pathway / protein autophosphorylation / protein kinase activity / protein serine/threonine kinase activity / lipid binding / negative regulation of apoptotic process / apoptotic process / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Extension to Ser/Thr-type protein kinases ...GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-453 / G protein-coupled receptor kinase 5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsHoman, K.T. / Tesmer, J.J.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
American Heart AssociationN014938 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of G Protein-coupled Receptor Kinase 5 in Complex with a Rationally Designed Inhibitor.
Authors: Homan, K.T. / Waldschmidt, H.V. / Glukhova, A. / Cannavo, A. / Song, J. / Cheung, J.Y. / Koch, W.J. / Larsen, S.D. / Tesmer, J.J.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G protein-coupled receptor kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6333
Polymers69,0381
Non-polymers5962
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.106, 70.104, 182.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomeric G protein coupled-receptor kinase 5 as evidenced by gel filtration

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Components

#1: Protein G protein-coupled receptor kinase 5 / G protein-coupled receptor kinase GRK5


Mass: 69037.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK5, GPRK5 / Plasmid: PFastBacDual / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P43249, G-protein-coupled receptor kinase
#2: Chemical ChemComp-453 / (4S)-4-{4-fluoro-3-[(pyridin-2-ylmethyl)carbamoyl]phenyl}-N-(1H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide


Mass: 499.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22FN7O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: HEPES, ethylene glycol, PEG 3350 / PH range: 7.25-7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.1271 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 24217 / Num. obs: 24217 / % possible obs: 99.9 % / Redundancy: 37.7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 42.3
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 34.8 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNK

4pnk


Resolution: 2.42→24.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 20.69 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 1235 5.1 %RANDOM
Rwork0.19379 ---
obs0.19635 22906 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.42→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 42 37 4146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194216
X-RAY DIFFRACTIONr_bond_other_d0.0010.024015
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9835677
X-RAY DIFFRACTIONr_angle_other_deg0.80539270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91923.575207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45815778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4111534
X-RAY DIFFRACTIONr_chiral_restr0.0820.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02995
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2644.0511998
X-RAY DIFFRACTIONr_mcbond_other2.2644.051997
X-RAY DIFFRACTIONr_mcangle_it3.3926.0722495
X-RAY DIFFRACTIONr_mcangle_other3.3916.0742496
X-RAY DIFFRACTIONr_scbond_it2.8384.3892218
X-RAY DIFFRACTIONr_scbond_other2.8264.3812215
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5116.4363175
X-RAY DIFFRACTIONr_long_range_B_refined5.88131.8514770
X-RAY DIFFRACTIONr_long_range_B_other5.84731.8344765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.425→2.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 89 -
Rwork0.232 1546 -
obs--96.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31121.4857-0.31096.4479-2.76685.0066-0.0338-0.116-0.37360.04220.34270.32610.5355-0.7602-0.30890.29210.00310.01380.44190.23510.1813-0.651-8.488-11.22
24.0408-0.22821.71451.6635-0.76482.2708-0.0850.1896-0.0233-0.06570.04820.0142-0.08970.08380.03680.15610.01240.06640.20720.04750.0429-6.68413.651-37.729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 180
2X-RAY DIFFRACTION1A506 - 575
4X-RAY DIFFRACTION2A181 - 505
5X-RAY DIFFRACTION2A701
6X-RAY DIFFRACTION2A702

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