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- PDB-6q7s: ERK2 mini-fragment binding -

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Basic information

Entry
Database: PDB / ID: 6q7s
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 / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated ...phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / Signaling by MAP2K mutants / response to epidermal growth factor / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of cellular pH / positive regulation of macrophage proliferation / regulation of Golgi inheritance / outer ear morphogenesis / Regulation of the apoptosome activity / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of cytoskeleton organization / regulation of stress-activated MAPK cascade / Frs2-mediated activation / IFNG signaling activates MAPKs / positive regulation of macrophage chemotaxis / response to exogenous dsRNA / lung morphogenesis / ERBB2-ERBB3 signaling pathway / face development / Recycling pathway of L1 / Activation of the AP-1 family of transcription factors / androgen receptor signaling pathway / ERK/MAPK targets / pseudopodium / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / positive regulation of telomere capping / negative regulation of cell differentiation / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate WASPs and WAVEs / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / stress-activated MAPK cascade / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / myelination / NPAS4 regulates expression of target genes / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / response to nicotine / positive regulation of peptidyl-threonine phosphorylation / Signal transduction by L1 / Regulation of PTEN gene transcription / long-term synaptic potentiation / caveola / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / B cell receptor signaling pathway / Spry regulation of FGF signaling / peptidyl-threonine phosphorylation / Signaling by high-kinase activity BRAF mutants / regulation of protein stability / MAP2K and MAPK activation / Oncogene Induced Senescence / mitotic spindle / 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. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...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
PHENOL / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.73 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 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release

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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)42,8364
Polymers42,5521
Non-polymers2843
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-4 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.628, 69.791, 60.169
Angle α, β, γ (deg.)90.00, 108.81, 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 / Sulfate


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


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 02M (NH4)2SO4 33% 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: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→56.95 Å / Num. obs: 33133 / % possible obs: 83.9 % / Redundancy: 2.8 % / Rrim(I) all: 0.057 / Net I/σ(I): 10.1
Reflection shellResolution: 1.73→1.75 Å / Num. unique obs: 887 / Rrim(I) all: 1.522 / % possible all: 75.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→56.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.501 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23988 1569 5.1 %RANDOM
Rwork0.18364 ---
obs0.1865 29054 76.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.31 Å2
2---0.69 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.73→56.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 19 312 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0152894
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172623
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.7613922
X-RAY DIFFRACTIONr_angle_other_deg0.4871.7256153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36321.324136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7815.381473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0851518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0213192
X-RAY DIFFRACTIONr_gen_planes_other00.02528
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_it2.4244.041373
X-RAY DIFFRACTIONr_mcbond_other2.4174.0381373
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3895.0171521
X-RAY DIFFRACTIONr_scbond_other3.3885.0211522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.48223.1263229
X-RAY DIFFRACTIONr_long_range_B_other6.4522.8593200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 34 -
Rwork0.373 522 -
obs--19.02 %
Refinement TLS params.Method: refined / Origin x: -0.7205 Å / Origin y: 3.5324 Å / Origin z: 38.0183 Å
111213212223313233
T0.0289 Å2-0.0046 Å20.0037 Å2-0.0236 Å2-0.0309 Å2--0.0408 Å2
L1.4069 °2-0.4989 °20.6557 °2-0.6031 °2-0.1399 °2--2.437 °2
S-0.0626 Å °-0.1594 Å °0.2139 Å °0.0798 Å °0.02 Å °-0.0249 Å °-0.213 Å °-0.0098 Å °0.0427 Å °

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