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- PDB-5bx0: An Automated Microscale Thermophoresis Screening Approach for Fra... -

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Basic information

Entry
Database: PDB / ID: 5bx0
TitleAn Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery
ComponentsDual specificity mitogen-activated protein kinase kinase 1
KeywordsTRANSFERASE / fragment screening / microscale thermophoresis
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / labyrinthine layer development / type B pancreatic cell proliferation / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / labyrinthine layer development / type B pancreatic cell proliferation / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants / regulation of Golgi inheritance / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / protein kinase activator activity / endodermal cell differentiation / face development / MAPK3 (ERK1) activation / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / Schwann cell development / keratinocyte differentiation / ERK1 and ERK2 cascade / myelination / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / cell motility / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / neuron differentiation / positive regulation of protein serine/threonine kinase activity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome / heart development / scaffold protein binding / protein tyrosine kinase activity / early endosome / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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, ATP binding site / Protein kinases ATP-binding region signature. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ethyl 2H-indazole-5-carboxylate / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsVallee, F. / Steier, V. / Rak, A.
CitationJournal: J Biomol Screen / Year: 2016
Title: An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery.
Authors: Linke, P. / Amaning, K. / Maschberger, M. / Vallee, F. / Steier, V. / Baaske, P. / Duhr, S. / Breitsprecher, D. / Rak, A.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 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

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1072
Polymers38,9171
Non-polymers1901
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.402, 75.402, 223.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 38916.879 Da / Num. of mol.: 1 / Fragment: residues 37-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-4W5 / ethyl 2H-indazole-5-carboxylate


Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 % / Description: rod-shaped crystals
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.65 / Details: PEG4000 20% CaCl2 200mM Glycerol 25% ph7.7 / PH range: 7.65

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.93→37.7 Å / Num. all: 8771 / Num. obs: 8771 / % possible obs: 99.7 % / Redundancy: 17.6 % / Biso Wilson estimate: 78.14 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 18.7
Reflection shellResolution: 2.93→3.28 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 4.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZLS

3zls


Resolution: 2.93→37.18 Å / Cor.coef. Fo:Fc: 0.8544 / Cor.coef. Fo:Fc free: 0.8421 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 448 5.14 %RANDOM
Rwork0.1973 ---
obs0.2003 8711 99.59 %-
Displacement parametersBiso mean: 94.55 Å2
Baniso -1Baniso -2Baniso -3
1--27.1981 Å20 Å20 Å2
2---27.1981 Å20 Å2
3---54.3962 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.93→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 14 0 2470
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012518HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173390HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d906SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes373HARMONIC5
X-RAY DIFFRACTIONt_it2518HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion20.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion317SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2838SEMIHARMONIC4
LS refinement shellResolution: 2.93→3.28 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3452 135 5.67 %
Rwork0.2377 2245 -
all0.2435 2380 -
obs--99.59 %

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