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- PDB-4pni: Bovine G protein-coupled receptor kinase 1 in complex with GSK2163632A -

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Basic information

Entry
Database: PDB / ID: 4pni
TitleBovine G protein-coupled receptor kinase 1 in complex with GSK2163632A
ComponentsRhodopsin kinase
KeywordsTransferase/Transferase inhibitor / AGC FAMILY KINASE / SER/THR KINASE / RGS HOMOLOGY DOMAIN / G PROTEIN COUPLED RECEPTOR KINASE / GRK / GRK1 / RHODOPSIN KINASE / HYDROLYASE / GPCR / PHOSPHORYLATION / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


rhodopsin kinase / rhodopsin kinase activity / regulation of rhodopsin mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein kinase activity / protein autophosphorylation / protein phosphorylation ...rhodopsin kinase / rhodopsin kinase activity / regulation of rhodopsin mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein kinase activity / protein autophosphorylation / protein phosphorylation / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain ...Rhodopsin kinase GRK1 / Rhodopsin kinase, catalytic domain / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / 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-KQQ / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsHoman, K.T. / Tesmer, J.J.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 and HL086865 United States
American Heart AssociationN014938 United States
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Identification and structure-function analysis of subfamily selective g protein-coupled receptor kinase inhibitors.
Authors: Homan, K.T. / Larimore, K.M. / Elkins, J.M. / Szklarz, M. / Knapp, S. / Tesmer, J.J.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7738
Polymers63,0121
Non-polymers7617
Water3,927218
1
A: Rhodopsin kinase
hetero molecules

A: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,54616
Polymers126,0242
Non-polymers1,52314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area4010 Å2
ΔGint-129 kcal/mol
Surface area45810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.485, 66.566, 205.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Rhodopsin kinase / / RK / G protein-coupled receptor kinase 1


Mass: 63011.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase
#2: Chemical ChemComp-KQQ / 3-[(2-{[1-(N,N-dimethylglycyl)-6-methoxy-4,4-dimethyl-1,2,3,4-tetrahydroquinolin-7-yl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]thiophene-2-carboxamide


Mass: 548.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32N8O3S
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES, PEG 3350, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 51503 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rsym value: 0.103 / Net I/σ(I): 90
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 19.5 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 1.85→24.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.259 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 2753 5.1 %RANDOM
Rwork0.18848 ---
obs0.19054 51503 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.22 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.85→24.67 Å / Total: 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194126
X-RAY DIFFRACTIONr_bond_other_d0.0010.023927
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.985578
X-RAY DIFFRACTIONr_angle_other_deg0.97139032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89823.596203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16915714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231533
X-RAY DIFFRACTIONr_chiral_restr0.1290.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214692
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02995
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_it4.2524.561989
X-RAY DIFFRACTIONr_mcbond_other4.254.561990
X-RAY DIFFRACTIONr_mcangle_it5.3446.8112488
X-RAY DIFFRACTIONr_mcangle_other5.3446.8112488
X-RAY DIFFRACTIONr_scbond_it5.2965.062137
X-RAY DIFFRACTIONr_scbond_other5.2955.062138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.77.3753091
X-RAY DIFFRACTIONr_long_range_B_refined9.23936.5594763
X-RAY DIFFRACTIONr_long_range_B_other9.24836.3854691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 208 -
Rwork0.277 3672 -
obs--98.2 %

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