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- PDB-5z1e: MAP2K7 C218S mutant-inhibitor -

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Basic information

Entry
Database: PDB / ID: 5z1e
TitleMAP2K7 C218S mutant-inhibitor
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / protein kinase
Function / homology
Function and homology information


JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / phosphorylation / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / enzyme binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-95U / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKinoshita, T. / London, N.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor.
Authors: Shraga, A. / Olshvang, E. / Davidzohn, N. / Khoshkenar, P. / Germain, N. / Shurrush, K. / Carvalho, S. / Avram, L. / Albeck, S. / Unger, T. / Lefker, B. / Subramanyam, C. / Hudkins, R.L. / ...Authors: Shraga, A. / Olshvang, E. / Davidzohn, N. / Khoshkenar, P. / Germain, N. / Shurrush, K. / Carvalho, S. / Avram, L. / Albeck, S. / Unger, T. / Lefker, B. / Subramanyam, C. / Hudkins, R.L. / Mitchell, A. / Shulman, Z. / Kinoshita, T. / London, N.
History
DepositionDec 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2602
Polymers36,9831
Non-polymers2771
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16340 Å2
Unit cell
Length a, b, c (Å)53.910, 70.830, 92.710
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 Dual specificity mitogen-activated protein kinase kinase 7 / MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase ...MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase kinase 4 / SAPKK4 / c-Jun N-terminal kinase kinase 2 / JNKK 2


Mass: 36982.836 Da / Num. of mol.: 1 / Fragment: UNP residues 103-419 / Mutation: C218S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Production host: Escherichia coli B (bacteria)
References: UniProt: O14733, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-95U / N-[3-(6-methyl-1H-indazol-3-yl)phenyl]prop-2-enamide


Mass: 277.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the conflict(SER,218A) is due to the expression artifact. (see SEQADV)

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium citrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.3→46.6 Å / Num. obs: 16329 / % possible obs: 99.8 % / Redundancy: 6.9 % / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.44 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y90

5y90


Resolution: 2.3→46.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.479 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28345 817 5 %RANDOM
Rwork0.19433 ---
obs0.19853 15512 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.195 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å20 Å2
2---0.63 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 2.3→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 21 116 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192439
X-RAY DIFFRACTIONr_bond_other_d0.0010.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9823281
X-RAY DIFFRACTIONr_angle_other_deg0.79535485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08723.738107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9091516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212678
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
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_it3.394.2391179
X-RAY DIFFRACTIONr_mcbond_other3.3894.2371178
X-RAY DIFFRACTIONr_mcangle_it5.286.3241465
X-RAY DIFFRACTIONr_mcangle_other5.2786.3281466
X-RAY DIFFRACTIONr_scbond_it4.0084.7451260
X-RAY DIFFRACTIONr_scbond_other4.0064.7471261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3616.9251817
X-RAY DIFFRACTIONr_long_range_B_refined8.97934.1572822
X-RAY DIFFRACTIONr_long_range_B_other8.9834.1472810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 58 -
Rwork0.313 1098 -
obs--98.47 %

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