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- PDB-5z1d: MAP2K7 C276S mutant-inhibitor -

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Basic information

Entry
Database: PDB / ID: 5z1d
TitleMAP2K7 C276S mutant-inhibitor
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / protein kinase
Function / homology
Function and homology information


regulation of motor neuron apoptotic process / JUN kinase kinase activity / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere maintenance / MAP kinase kinase activity / Uptake and function of anthrax toxins / cellular response to interleukin-1 / response to tumor necrosis factor ...regulation of motor neuron apoptotic process / JUN kinase kinase activity / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere maintenance / MAP kinase kinase activity / Uptake and function of anthrax toxins / cellular response to interleukin-1 / response to tumor necrosis factor / positive regulation of JUN kinase activity / MAP kinase activity / response to UV / stress-activated MAPK cascade / JNK cascade / molecular function activator activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / cellular response to lipopolysaccharide / protein tyrosine kinase activity / protein phosphatase binding / Oxidative Stress Induced Senescence / positive regulation of ERK1 and ERK2 cascade / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
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: 2.28 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn
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)37,4983
Polymers36,9831
Non-polymers5162
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint3 kcal/mol
Surface area13450 Å2
Unit cell
Length a, b, c (Å)54.584, 63.827, 88.458
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: 36982.840 Da / Num. of mol.: 1 / Fragment: UNP residues 103-419 / Mutation: C276S
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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the conflict(SER,270A) 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: 2.08 Å3/Da / Density % sol: 40.96 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.28→51.8 Å / Num. obs: 14635 / % possible obs: 98.8 % / Redundancy: 6.4 % / Net I/σ(I): 10.2
Reflection shellResolution: 2.28→2.36 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: 2.28→51.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.616 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25806 704 4.8 %RANDOM
Rwork0.19227 ---
obs0.19544 13893 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å2-0 Å20 Å2
2--1.5 Å20 Å2
3----3.32 Å2
Refinement stepCycle: 1 / Resolution: 2.28→51.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 36 101 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192277
X-RAY DIFFRACTIONr_bond_other_d0.0020.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.993057
X-RAY DIFFRACTIONr_angle_other_deg0.91335156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62623.83899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97615430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9041515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212482
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022511
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_it3.3844.2361092
X-RAY DIFFRACTIONr_mcbond_other3.3814.2321091
X-RAY DIFFRACTIONr_mcangle_it4.8396.3311358
X-RAY DIFFRACTIONr_mcangle_other4.8386.3351359
X-RAY DIFFRACTIONr_scbond_it4.5844.8911185
X-RAY DIFFRACTIONr_scbond_other4.5844.8911185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9997.0921700
X-RAY DIFFRACTIONr_long_range_B_refined9.47334.9942686
X-RAY DIFFRACTIONr_long_range_B_other9.47235.0122687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 40 -
Rwork0.249 1010 -
obs--100 %

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