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- PDB-4wbo: Bovine G Protein Coupled Receptor Kinase 1 in Complex with Amlexanox -

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Basic information

Entry
Database: PDB / ID: 4wbo
TitleBovine G Protein Coupled Receptor Kinase 1 in Complex with Amlexanox
ComponentsRhodopsin kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / G-Protein-Coupled Receptor Kinase 1 / Amlexanox / Phosphorylation / Protein Conformation / Protein Kinase Inhibitors / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein autophosphorylation / signal transduction / ATP binding / cytoplasm
Similarity search - Function
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 ...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. / 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-ANW / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.81 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, HL086865 United States
American Heart AssociationN014938 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P60DK020572 United States
CitationJournal: Molecules / Year: 2014
Title: Identification and characterization of amlexanox as a g protein-coupled receptor kinase 5 inhibitor.
Authors: Homan, K.T. / Wu, E. / Cannavo, A. / Koch, W.J. / Tesmer, J.J.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / 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_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin kinase
B: Rhodopsin kinase
C: Rhodopsin kinase
D: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,19812
Polymers244,8634
Non-polymers1,3358
Water97354
1
A: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5493
Polymers61,2161
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5493
Polymers61,2161
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5493
Polymers61,2161
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5493
Polymers61,2161
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.112, 119.166, 174.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA30 - 53230 - 532
21SERSERARGARGBB30 - 53230 - 532
12ARGARGTRPTRPAA31 - 53131 - 531
22ARGARGTRPTRPCC31 - 53131 - 531
13SERSERTRPTRPAA30 - 53130 - 531
23SERSERTRPTRPDD30 - 53130 - 531
14ARGARGTRPTRPBB31 - 53131 - 531
24ARGARGTRPTRPCC31 - 53131 - 531
15SERSERTRPTRPBB30 - 53130 - 531
25SERSERTRPTRPDD30 - 53130 - 531
16ARGARGTRPTRPCC31 - 53131 - 531
26ARGARGTRPTRPDD31 - 53131 - 531

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 61215.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Plasmid: PFastBac / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase
#2: Chemical
ChemComp-ANW / 2-amino-7-(1-methylethyl)-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid / Amlexanox


Mass: 298.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14N2O4 / Comment: antiinflammatory*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25 / Details: 500 mM NaCl, 100 mM MES pH 6.25, and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.82→25 Å / Num. obs: 60016 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.5
Reflection shellResolution: 2.82→2.87 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 2.81→24.89 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.916 / SU B: 33.617 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26726 3023 5 %RANDOM
Rwork0.24149 ---
obs0.24277 56928 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.81→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15786 0 92 54 15932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01916255
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215522
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.97621938
X-RAY DIFFRACTIONr_angle_other_deg0.906335692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69951955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47223.596801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.984152832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.10715129
X-RAY DIFFRACTIONr_chiral_restr0.0530.22289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02118378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023883
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_it1.1914.5137847
X-RAY DIFFRACTIONr_mcbond_other1.1914.5137846
X-RAY DIFFRACTIONr_mcangle_it2.0796.7659793
X-RAY DIFFRACTIONr_mcangle_other2.0796.7659794
X-RAY DIFFRACTIONr_scbond_it1.0024.5488408
X-RAY DIFFRACTIONr_scbond_other1.0024.5488406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8076.78912143
X-RAY DIFFRACTIONr_long_range_B_refined3.67534.97418128
X-RAY DIFFRACTIONr_long_range_B_other3.67534.97418129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A30113
12B30113
21A29291
22C29291
31A29901
32D29901
41B29480
42C29480
51B30036
52D30036
61C29325
62D29325
LS refinement shellResolution: 2.815→2.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 236 -
Rwork0.406 3886 -
obs--94.8 %
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)
17.7036-0.6956-0.12634.32760.65151.0876-0.1780.25010.26490.04150.1442-0.10860.16090.1860.03380.2304-0.0449-0.05150.2520.03590.027351.9027-79.0434-19.4556
24.7687-1.2569-0.91567.3329-1.61244.91130.2258-0.09890.70780.05680.05970.994-0.821-0.1733-0.28550.328-0.0320.08330.2153-0.03490.53535.1072-53.6976-11.033
34.6842-0.69760.98998.6284-0.87344.5409-0.1627-0.32510.73770.70980.1057-1.16190.01730.26380.05690.12920.0701-0.08720.3553-0.15130.660859.1964-46.3814-6.3378
43.3781-1.44653.0147.2939-1.16115.2724-0.089-0.0708-0.2743-0.10010.17880.5256-0.0920.0102-0.08980.184100.04230.20770.010.0668-27.4212-76.992418.2751
56.4162-1.91541.17285.5327-1.51115.5552-0.5961-1.4511.16232.03610.3028-1.0832-1.05110.4970.29320.97470.0219-0.35990.7305-0.31580.4916-12.2512-54.902935.5357
63.7492-1.2892.84839.3985-2.26917.12360.12550.0937-0.14130.21450.23830.55060.0429-0.0913-0.36380.2875-0.00090.06180.14-0.04410.240628.1086-69.153922.6194
74.39010.51781.51515.3771.15563.20520.2604-0.94580.35852.50240.0774-0.29320.10890.0833-0.33781.51-0.0699-0.20570.5243-0.12020.62438.3619-47.989442.6119
83.1828-0.74870.18317.15910.32754.709-0.15990.10640.06280.71810.0206-0.1582-0.4176-0.31630.13930.5379-0.02310.08850.2556-0.03850.203325.6896-32.684826.5148
96.1466-1.505-0.97045.37622.0382.8092-0.21460.11760.0113-0.24960.2691-1.12370.410.5482-0.05440.35340.10150.08170.29360.07650.4532-10.3937-87.448-27.0155
105.5465-2.3497-0.62769.6803-1.29356.21270.0703-0.13180.76690.12530.1395-0.4091-0.90050.0039-0.20990.1952-0.0079-0.00760.18990.00440.1589-25.3506-61.2923-15.9968
114.63080.59570.43587.74980.27913.9402-0.1072-0.3130.29790.34150.4961-1.8231-0.47390.8994-0.38890.3141-0.0468-0.03930.7185-0.22821.0874-0.9273-54.443-14.1362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 184
2X-RAY DIFFRACTION1A512 - 533
3X-RAY DIFFRACTION2A185 - 268
4X-RAY DIFFRACTION2A478 - 511
5X-RAY DIFFRACTION2A601
6X-RAY DIFFRACTION3A269 - 477
7X-RAY DIFFRACTION4B30 - 184
8X-RAY DIFFRACTION4B512 - 533
9X-RAY DIFFRACTION5B185 - 268
10X-RAY DIFFRACTION5B478 - 511
11X-RAY DIFFRACTION5B601
12X-RAY DIFFRACTION6C31 - 184
13X-RAY DIFFRACTION6C512 - 531
14X-RAY DIFFRACTION7C185 - 268
15X-RAY DIFFRACTION7C494 - 511
16X-RAY DIFFRACTION7C601
17X-RAY DIFFRACTION8C269 - 473
18X-RAY DIFFRACTION9D30 - 184
19X-RAY DIFFRACTION9D512 - 531
20X-RAY DIFFRACTION10D185 - 268
21X-RAY DIFFRACTION10D478 - 511
22X-RAY DIFFRACTION10D601
23X-RAY DIFFRACTION11D269 - 477

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