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- PDB-6qg7: Structure of the mitogen activated kinase kinase 7 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6qg7
TitleStructure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine 1k
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 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6HL / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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

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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)36,5452
Polymers36,1471
Non-polymers3981
Water1,71195
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 area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 65.800, 86.000
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-6HL / (R)-1-(3-(4-amino-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one


Mass: 398.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
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: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 23272 / % possible obs: 99.7 % / Redundancy: 11.64 % / CC1/2: 0.999 / Rrim(I) all: 0.129 / Rsym value: 0.123 / Net I/σ(I): 13.21
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.97 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3038 / CC1/2: 0.134 / Rrim(I) all: 0.859 / Rsym value: 0.815 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.1→44.092 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1420 7 %Random selection
Rwork0.2337 ---
obs0.2361 20276 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 30 95 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032236
X-RAY DIFFRACTIONf_angle_d0.7013022
X-RAY DIFFRACTIONf_dihedral_angle_d2.1551331
X-RAY DIFFRACTIONf_chiral_restr0.042335
X-RAY DIFFRACTIONf_plane_restr0.004383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.40751400.37521836X-RAY DIFFRACTION100
2.1751-2.26210.36771390.33421866X-RAY DIFFRACTION100
2.2621-2.36510.36081390.31811855X-RAY DIFFRACTION100
2.3651-2.48980.33031390.29491849X-RAY DIFFRACTION100
2.4898-2.64570.31751410.28381854X-RAY DIFFRACTION100
2.6457-2.850.33891410.26441889X-RAY DIFFRACTION100
2.85-3.13670.29181410.25011876X-RAY DIFFRACTION100
3.1367-3.59040.25891430.22461893X-RAY DIFFRACTION100
3.5904-4.52280.23931450.18691921X-RAY DIFFRACTION100
4.5228-44.10130.20151520.1882017X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.053 Å / Origin y: 9.2003 Å / Origin z: -12.9136 Å
111213212223313233
T0.2384 Å20.0607 Å2-0.008 Å2-0.2197 Å2-0.0684 Å2--0.2423 Å2
L1.6446 °21.1267 °2-0.2863 °2-1.3882 °2-0.3325 °2--1.1937 °2
S-0.027 Å °0.086 Å °-0.2377 Å °-0.0108 Å °0.0503 Å °-0.1662 Å °0.0974 Å °0.0937 Å °-0.0223 Å °
Refinement TLS groupSelection details: all

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