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- PDB-6qhr: Structure of the mitogen activated kinase kinase 7 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6qhr
TitleStructure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine 1m
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / Protein Kinase / Kinase / MKK7
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 / MAP kinase kinase activity / response to tumor necrosis factor / positive regulation of telomere maintenance / Uptake and function of anthrax toxins / MAP kinase activity ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to tumor necrosis factor / positive regulation of telomere maintenance / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / stress-activated MAPK cascade / response to UV / JNK cascade / molecular function activator activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of JNK cascade / FCERI mediated MAPK activation / response to wounding / cellular senescence / cellular response to lipopolysaccharide / response to heat / 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-J3N / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsWolle, P. / Mueller, M.P. / Rauh, D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Characterization of Covalent Pyrazolopyrimidine-MKK7 Complexes and a Report on a Unique DFG-in/Leu-in Conformation of Mitogen-Activated Protein Kinase Kinase 7 (MKK7).
Authors: Wolle, P. / Engel, J. / Smith, S. / Goebel, L. / Hennes, E. / Lategahn, J. / Rauh, D.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.4Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Jan 24, 2024Group: 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 1.6Nov 6, 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: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5372
Polymers36,1471
Non-polymers3901
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 69.000, 84.900
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: 36146.859 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria)
References: UniProt: O14733, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-J3N / 1-[(3~{R})-3-[4-azanyl-3-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one


Mass: 390.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodiumcitrate 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.4→46.159 Å / Num. obs: 14025 / % possible obs: 94.8 % / Redundancy: 12.5 % / CC1/2: 0.912 / Rrim(I) all: 0.42 / Rsym value: 0.4 / Net I/σ(I): 4.82
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 1642 / CC1/2: 0.9 / Rrim(I) all: 0.96 / Rsym value: 0.92 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dyl

2dyl


Resolution: 2.52→46.159 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2938 883 6.98 %Random selection
Rwork0.237 ---
obs0.2409 12648 98.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→46.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 29 92 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032255
X-RAY DIFFRACTIONf_angle_d0.6873052
X-RAY DIFFRACTIONf_dihedral_angle_d13.3211342
X-RAY DIFFRACTIONf_chiral_restr0.042338
X-RAY DIFFRACTIONf_plane_restr0.004390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5201-2.6780.33591460.24631941X-RAY DIFFRACTION100
2.678-2.88470.3011470.25421953X-RAY DIFFRACTION100
2.8847-3.1750.30661470.2471958X-RAY DIFFRACTION100
3.175-3.63420.32951460.28271934X-RAY DIFFRACTION98
3.6342-4.57810.32981390.25311880X-RAY DIFFRACTION94
4.5781-46.16630.21541580.18332099X-RAY DIFFRACTION100

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