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- PDB-6opi: phosphorylated ERK2 with SCH-CPD336 -

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Basic information

Entry
Database: PDB / ID: 6opi
Titlephosphorylated ERK2 with SCH-CPD336
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / ERK 2 / MITOGEN ACTIVATED PROTEIN KINASE 2 / MAP KINASE 2 / SIGNALING PROTEIN
Function / homology
Function and homology information


phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / Signaling by MAP2K mutants / Signaling by NODAL / response to epidermal growth factor / ERKs are inactivated / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / positive regulation of macrophage chemotaxis / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / response to exogenous dsRNA / face development / MAPK1 (ERK2) activation / lung morphogenesis / positive regulation of telomere maintenance / Recycling pathway of L1 / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / peptidyl-threonine phosphorylation / RHO GTPases Activate NADPH Oxidases / negative regulation of cell differentiation / regulation of ossification / MAP kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / Regulation of HSF1-mediated heat shock response / mitogen-activated protein kinase / Signal attenuation / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / myelination / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / cellular response to amino acid starvation / Negative regulation of FGFR3 signaling / ESR-mediated signaling / lipopolysaccharide-mediated signaling pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / thymus development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of PTEN gene transcription / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signal transduction by L1 / Spry regulation of FGF signaling / response to nicotine / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Oncogene Induced Senescence / FCERI mediated MAPK activation / positive regulation of cholesterol biosynthetic process / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / caveola / Regulation of actin dynamics for phagocytic cup formation / Negative regulation of MAPK pathway / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / chemotaxis
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-N0V / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVigers, G.P. / Smith, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM114594 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10RR026641 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32GM008759 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2.
Authors: Pegram, L.M. / Liddle, J.C. / Xiao, Y. / Hoh, M. / Rudolph, J. / Iverson, D.B. / Vigers, G.P. / Smith, D. / Zhang, H. / Wang, W. / Moffat, J.G. / Ahn, N.G.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8032
Polymers41,1341
Non-polymers6691
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.394, 77.640, 126.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK ...MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAPK 2


Mass: 41134.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Chemical ChemComp-N0V / (3R)-N-[3-(2-cyclopropylpyridin-4-yl)-1H-indazol-5-yl]-3-(methoxymethyl)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]-3,6-dihydropyridin-1(2H)-yl}ethyl)pyrrolidine-3-carboxamide


Mass: 668.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H40N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% (w/v) PEG3350, 100 mM Na cacodylate pH 7.2, 600 mM NaCl, 10 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 25, 2008 / Details: Osmic confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 8550 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1248 / Rpim(I) all: 0.177 / Rrim(I) all: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ERK

2erk


Resolution: 3→22.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.683 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.459 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26046 410 4.7 %RANDOM
Rwork0.18489 ---
obs0.18852 8226 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.605 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2--0.1 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: 1 / Resolution: 3→22.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 50 30 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172567
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6733768
X-RAY DIFFRACTIONr_angle_other_deg1.1871.5765968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3955322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7322.467150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1271518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02551
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_it3.7064.8931300
X-RAY DIFFRACTIONr_mcbond_other3.6984.8921299
X-RAY DIFFRACTIONr_mcangle_it5.77.3211618
X-RAY DIFFRACTIONr_mcangle_other5.6997.3221619
X-RAY DIFFRACTIONr_scbond_it3.6785.1111479
X-RAY DIFFRACTIONr_scbond_other3.6965.1611423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8297.6352069
X-RAY DIFFRACTIONr_long_range_B_refined8.00256.0223110
X-RAY DIFFRACTIONr_long_range_B_other8.04556.4443026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 29 -
Rwork0.247 578 -
obs--100 %

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