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- PDB-6oph: phosphorylated ERK2 with GDC-0994 -

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Basic information

Entry
Database: PDB / ID: 6oph
Titlephosphorylated ERK2 with GDC-0994
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / SIGNALING PROTEIN
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cytosine metabolic process / cardiac neural crest cell development involved in heart development / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cytosine metabolic process / cardiac neural crest cell development involved in heart development / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / RSK activation / ERKs are inactivated / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / outer ear morphogenesis / : / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / Signaling by LTK in cancer / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / ERBB signaling pathway / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / positive regulation of neuroinflammatory response / Frs2-mediated activation / Activation of the AP-1 family of transcription factors / ERBB2-ERBB3 signaling pathway / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / ERK/MAPK targets / MAPK1 (ERK2) activation / regulation of cytoskeleton organization / positive regulation of macrophage chemotaxis / face development / Bergmann glial cell differentiation / Recycling pathway of L1 / thyroid gland development / positive regulation of telomere maintenance / pseudopodium / lung morphogenesis / Advanced glycosylation endproduct receptor signaling / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of cell differentiation / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / stress-activated MAPK cascade / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / Nuclear events stimulated by ALK signaling in cancer / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ciliary tip / thymus development / cellular response to amino acid starvation / Regulation of PTEN gene transcription / chemokine-mediated signaling pathway / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / positive regulation of cholesterol biosynthetic process / MAP2K and MAPK activation / Negative Regulation of CDH1 Gene Transcription / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / caveola / cellular response to tumor necrosis factor / epidermal growth factor receptor signaling pathway
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
Chem-6QB / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)41,5752
Polymers41,1341
Non-polymers4411
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.070, 76.930, 151.760
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-6QB / 1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]pyridin-2-one


Mass: 440.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18ClFN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 36% PEG3350, 100mM bicine pH 9.0

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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: Mar 28, 2012 / Details: osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 17814 / % possible obs: 88.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.294 / Num. unique obs: 1835 / Rpim(I) all: 0.121 / Rrim(I) all: 0.319 / Χ2: 2.6 / % possible all: 69.4

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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: 2.4→26.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.848 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.256 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24287 904 5.1 %RANDOM
Rwork0.19291 ---
obs0.19536 16861 88.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--3.13 Å2-0 Å2
3----3.32 Å2
Refinement stepCycle: 1 / Resolution: 2.4→26.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 31 17 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172718
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6624014
X-RAY DIFFRACTIONr_angle_other_deg1.2011.5756319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69722.516159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90315518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8171518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_it4.2965.7641391
X-RAY DIFFRACTIONr_mcbond_other4.2925.7621390
X-RAY DIFFRACTIONr_mcangle_it5.9798.6451737
X-RAY DIFFRACTIONr_mcangle_other5.9798.6481738
X-RAY DIFFRACTIONr_scbond_it4.9096.2161567
X-RAY DIFFRACTIONr_scbond_other4.8396.231534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1469.172230
X-RAY DIFFRACTIONr_long_range_B_refined8.7265.9493206
X-RAY DIFFRACTIONr_long_range_B_other8.54866.1983148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 52 -
Rwork0.227 919 -
obs--66.64 %

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