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

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Basic information

Entry
Database: PDB / ID: 6qft
TitleStructure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidin 1b
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / Protein Kinase / Kinase / MKK7
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 / MAP kinase kinase activity / positive regulation of telomere maintenance / 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 / MAP kinase kinase activity / positive regulation of telomere maintenance / Uptake and function of anthrax toxins / cellular response to interleukin-1 / response to tumor necrosis factor / MAP kinase activity / response to UV / stress-activated MAPK cascade / positive regulation of JUN kinase activity / 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 phosphatase binding / Oxidative Stress Induced Senescence / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / 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
: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-J0B / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 10, 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 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 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 1.4Jan 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 1.5Nov 13, 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)36,5472
Polymers36,1471
Non-polymers4001
Water61334
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 area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 67.100, 85.000
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-J0B / 1-[(3~{R})-3-(4-azanyl-3-iodanyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one


Mass: 400.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17IN6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
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: 1.5 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.7→49.235 Å / Num. obs: 9940 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rrim(I) all: 0.096 / Rsym value: 0.088 / Net I/σ(I): 16.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 997 / CC1/2: 0.885 / Rrim(I) all: 0.953 / Rsym value: 0.877 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYL

2dyl


Resolution: 2.7→49.235 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 871 7 %Random selection
Rwork0.2361 ---
obs0.2396 9940 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 21 34 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022174
X-RAY DIFFRACTIONf_angle_d0.6562940
X-RAY DIFFRACTIONf_dihedral_angle_d13.4551296
X-RAY DIFFRACTIONf_chiral_restr0.039329
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.40231420.351880X-RAY DIFFRACTION100
2.6566-2.86170.34421410.31081884X-RAY DIFFRACTION100
2.8617-3.14970.32171440.29641910X-RAY DIFFRACTION100
3.1497-3.60530.35651440.25961920X-RAY DIFFRACTION100
3.6053-4.54180.24941460.2031938X-RAY DIFFRACTION100
4.5418-49.2450.24951540.20452039X-RAY DIFFRACTION100

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