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- PDB-6qah: ERK2 mini-fragment binding -

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Basic information

Entry
Database: PDB / ID: 6qah
TitleERK2 mini-fragment binding
ComponentsMitogen-activated protein kinase 1
KeywordsSIGNALING PROTEIN / Ser/Thr kinase / signal transduction / ATP binding
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / ERKs are inactivated / cytosine metabolic process / Signaling by MAP2K mutants / Signaling by NODAL / response to epidermal growth factor / 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 / labyrinthine layer blood vessel development / ERBB signaling pathway / mammary gland epithelial cell proliferation / Negative feedback regulation of MAPK pathway / trachea formation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / Frs2-mediated activation / IFNG signaling activates MAPKs / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytoskeleton organization / response to exogenous dsRNA / lung morphogenesis / RUNX2 regulates osteoblast differentiation / face development / positive regulation of telomere maintenance / MAPK1 (ERK2) activation / Recycling pathway of L1 / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / negative regulation of cell differentiation / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / regulation of ossification / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / mitogen-activated protein kinase / JUN kinase activity / phosphatase binding / Signal attenuation / progesterone receptor signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / positive regulation of peptidyl-threonine phosphorylation / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / ERK1 and ERK2 cascade / NCAM signaling for neurite out-growth / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / ESR-mediated signaling / thymus development / Signal transduction by L1 / Regulation of PTEN gene transcription / peptidyl-threonine phosphorylation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / response to nicotine / FCERI mediated MAPK activation / long-term synaptic potentiation / 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 / positive regulation of cholesterol biosynthetic process / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / Oncogene Induced Senescence / caveola / Regulation of actin dynamics for phagocytic cup formation
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-azanylpropylideneazanium / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsO'Reilly, M. / Cleasby, A. / Davies, T.G. / Hall, R. / Ludlow, F. / Murray, C.W. / Tisi, D. / Jhoti, H.
CitationJournal: Drug Discov Today / Year: 2019
Title: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design.
Authors: O'Reilly, M. / Cleasby, A. / Davies, T.G. / Hall, R.J. / Ludlow, R.F. / Murray, C.W. / Tisi, D. / Jhoti, H.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,7944
Polymers42,5521
Non-polymers2423
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-13 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.742, 69.782, 60.599
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211

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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: 42551.922 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 BL21(DE3) (bacteria)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HVB / 1-azanylpropylideneazanium


Mass: 73.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M (NH4)2SO4 34% MPEG 2000 0.02M Mercaptoethanol 0.1M pH=7.2 HEPES/NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.58→48.74 Å / Num. obs: 37802 / % possible obs: 72.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 21.81 Å2 / Rrim(I) all: 0.037 / Net I/σ(I): 15.5
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 118 / Rrim(I) all: 1.261 / % possible all: 6.3

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→34.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1927 5.14 %RANDOM
Rwork0.181 ---
obs0.182 37496 71.8 %-
Displacement parametersBiso mean: 29.596 Å2
Baniso -1Baniso -2Baniso -3
1--0.9011 Å20 Å20.3169 Å2
2---0.1868 Å20 Å2
3---1.0879 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.58→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 25 244 3030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0145694HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1210311HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1262SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes916HARMONIC16
X-RAY DIFFRACTIONt_it5688HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.72
X-RAY DIFFRACTIONt_other_torsion15.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6447SEMIHARMONIC4
LS refinement shellResolution: 1.58→1.68 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.331 -5.2 %
Rwork0.2389 711 -
all0.2433 750 -
obs--8.75 %
Refinement TLS params.Method: refined / Origin x: -1.3833 Å / Origin y: 3.3211 Å / Origin z: 37.7164 Å
111213212223313233
T-0.0624 Å2-0.0106 Å20.0174 Å2--0.0862 Å2-0.018 Å2---0.0355 Å2
L0.9 °2-0.2709 °20.1547 °2-0.6525 °2-0.2777 °2--0.8246 °2
S-0.0305 Å °-0.0815 Å °0.1052 Å °0.1287 Å °0.0419 Å °0.0023 Å °-0.0966 Å °0.0225 Å °-0.0114 Å °
Refinement TLS groupSelection details: { A|11 - A|365 }

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