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- PDB-3gc8: The structure of p38beta C162S in complex with a dihydroquinazolinone -

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Basic information

Entry
Database: PDB / ID: 3gc8
TitleThe structure of p38beta C162S in complex with a dihydroquinazolinone
ComponentsMitogen-activated protein kinase 11
KeywordsTRANSFERASE / Serine/thronine kinase / drug design / selectivity / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors ...negative regulation of cardiac muscle cell proliferation / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cardiac muscle cell proliferation / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cellular response to UV-B / positive regulation of muscle cell differentiation / Myogenesis / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / positive regulation of interleukin-12 production / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / bone development / cellular response to virus / VEGFA-VEGFR2 Pathway / osteoblast differentiation / cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-B45 / NICKEL (II) ION / Mitogen-activated protein kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsScapin, G. / Patel, S.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The three-dimensional structure of MAP kinase p38beta: different features of the ATP-binding site in p38beta compared with p38alpha.
Authors: Patel, S.B. / Cameron, P.M. / O'Keefe, S.J. / Frantz-Wattley, B. / Thompson, J. / O'Neill, E.A. / Tennis, T. / Liu, L. / Becker, J.W. / Scapin, G.
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 11
B: Mitogen-activated protein kinase 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2927
Polymers84,0942
Non-polymers1,1985
Water3,495194
1
A: Mitogen-activated protein kinase 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6173
Polymers42,0471
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6754
Polymers42,0471
Non-polymers6293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.124, 157.710, 60.360
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 11 / Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / p38-2 / Stress-activated ...Mitogen-activated protein kinase p38 beta / MAP kinase p38 beta / p38b / p38-2 / Stress-activated protein kinase 2


Mass: 42046.844 Da / Num. of mol.: 2 / Mutation: C162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK11, PRKM11, SAPK2 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q15759, mitogen-activated protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-B45 / 5-(2-chloro-4-fluorophenyl)-1-(2,6-dichlorophenyl)-7-[1-(1-methylethyl)piperidin-4-yl]-3,4-dihydroquinazolin-2(1H)-one


Mass: 546.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27Cl3FN3O
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 3350, 0.12 M ammonium fluoride, 30 uM CTAB, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 28873 / Num. obs: 28642 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.088 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 2885 / Rsym value: 0.336 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GC7

3gc7


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.89 / SU B: 17.568 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.61 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27192 1440 5.1 %RANDOM
Rwork0.20842 ---
obs0.21171 27046 99.8 %-
all-27095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.04 Å2
2---0.74 Å20 Å2
3---1.17 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.324 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 75 194 5754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225691
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.987736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26423.588262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18415952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5931544
X-RAY DIFFRACTIONr_chiral_restr0.0890.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024428
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22493
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.53466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20525570
X-RAY DIFFRACTIONr_scbond_it1.66532312
X-RAY DIFFRACTIONr_scangle_it2.6424.52166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.565 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 237 -
Rwork0.229 4901 -
obs-5138 99.92 %
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)
11.18680.27140.5851.8699-0.7632.1047-0.0107-0.059-0.1071-0.03490.02370.26540.1486-0.3087-0.01290.05730.03710.034-0.0225-0.0182-0.024721.6038-16.529227.5628
22.8702-0.760.15062.32220.20012.05420.0148-0.0805-0.06440.0389-0.0430.06050.0717-0.06190.0282-0.1833-0.02040.0021-0.13050.0148-0.167929.470111.064430.3838
332.3676-6.80611.47191.9156-3.699723.7922-0.2031-2.2627-0.57720.0961-0.45710.15470.7797-1.3560.66020.1033-0.1384-0.06970.03430.07320.226726.1587-8.28135.8532
40.91870.1776-1.24771.6476-0.32312.2580.05270.05790.0733-0.0049-0.07920.3822-0.0976-0.35510.02650.0392-0.0068-0.0121-0.0157-0.05070.01228.060652.85532.2324
52.93090.75960.58083.39550.36412.65110.0262-0.07530.0446-0.0303-0.05910.1820.0297-0.20790.0329-0.19730.03750.0004-0.13910.0122-0.147215.376425.0496-0.3481
673.41494.6538-6.95761.28046.283646.54820.56922.47630.9310.2138-0.6561-0.9142-0.1679-1.33310.08690.09040.0846-0.01650.0330.12840.184612.47744.5884-6.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 112
2X-RAY DIFFRACTION1A323 - 349
3X-RAY DIFFRACTION2A115 - 320
4X-RAY DIFFRACTION3A365
5X-RAY DIFFRACTION4B4 - 112
6X-RAY DIFFRACTION4B323 - 349
7X-RAY DIFFRACTION5B115 - 320
8X-RAY DIFFRACTION6B365

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