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- PDB-5es1: CRYSTAL STRUCTURE OF MICROTUBULE AFFINITY-REGULATING KINASE 4 CAT... -

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Basic information

Entry
Database: PDB / ID: 5es1
TitleCRYSTAL STRUCTURE OF MICROTUBULE AFFINITY-REGULATING KINASE 4 CATALYTIC DOMAIN IN COMPLEX WITH A PYRAZOLOPYRIMIDINE INHIBITOR
ComponentsMAP/microtubule affinity-regulating kinase 4
KeywordsTransferase/Transferase Inhibitor / MARK4 PAR-1 SERINE/THREONINE PROTEIN KINASE11 / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / protein serine/threonine kinase activity => GO:0004674 / cilium organization / gamma-tubulin complex / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / regulation of centrosome cycle / microtubule bundle formation / gamma-tubulin binding / positive regulation of programmed cell death ...ciliary basal body-plasma membrane docking / protein serine/threonine kinase activity => GO:0004674 / cilium organization / gamma-tubulin complex / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / regulation of centrosome cycle / microtubule bundle formation / gamma-tubulin binding / positive regulation of programmed cell death / microtubule organizing center / tau-protein kinase activity / Anchoring of the basal body to the plasma membrane / ciliary basal body / ubiquitin binding / tau protein binding / microtubule cytoskeleton organization / microtubule cytoskeleton / nervous system development / midbody / microtubule binding / non-specific serine/threonine protein kinase / intracellular signal transduction / neuron projection / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / ATP binding / cytoplasm / cytosol
Similarity search - Function
Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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
Similarity search - Domain/homology
Chem-5RC / MAP/microtubule affinity-regulating kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSack, J.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of microtubule affinity-regulating kinase 4 catalytic domain in complex with a pyrazolopyrimidine inhibitor.
Authors: Sack, J.S. / Gao, M. / Kiefer, S.E. / Myers, J.E. / Newitt, J.A. / Wu, S. / Yan, C.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 27, 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: MAP/microtubule affinity-regulating kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0932
Polymers37,6191
Non-polymers4731
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.478, 111.478, 69.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein MAP/microtubule affinity-regulating kinase 4 / MAP/microtubule affinity-regulating kinase-like 1


Mass: 37619.363 Da / Num. of mol.: 1 / Fragment: CATALYTIC AND UBA DOMAINS, RESIDUES 44-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK4, KIAA1860, MARKL1 / Plasmid: pET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3
References: UniProt: Q96L34, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5RC / ~{N}-[(1~{R},6~{R})-6-azanyl-2,2-bis(fluoranyl)cyclohexyl]-5-ethyl-4-[6-(trifluoromethyl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide


Mass: 473.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F5N5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5 / Details: 20% (w/v) PEG 6000, 0.2 M MgCl2, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12441 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 101.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 3.9 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FE3

3fe3


Resolution: 2.8→36.49 Å / Cor.coef. Fo:Fc: 0.9097 / Cor.coef. Fo:Fc free: 0.857 / SU R Cruickshank DPI: 0.573 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.522 / SU Rfree Blow DPI: 0.36 / SU Rfree Cruickshank DPI: 0.374
RfactorNum. reflection% reflectionSelection details
Rfree0.3109 657 5.29 %RANDOM
Rwork0.239 11769 --
obs0.2426 12426 98.96 %-
Displacement parametersBiso max: 168.26 Å2 / Biso mean: 98.68 Å2 / Biso min: 62.57 Å2
Baniso -1Baniso -2Baniso -3
1-19.961 Å20 Å20 Å2
2--19.961 Å20 Å2
3----39.9221 Å2
Refine analyzeLuzzati coordinate error obs: 0.435 Å
Refinement stepCycle: final / Resolution: 2.8→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 32 8 2325
Biso mean--77.7 98.35 -
Num. residues----304
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d780SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes371HARMONIC5
X-RAY DIFFRACTIONt_it2365HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion320SEMIHARMONIC5
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_contact2673SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2365HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3227HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion19.48
LS refinement shellResolution: 2.8→3.04 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3172 156 5.43 %
Rwork0.2706 2716 -
all0.2733 2872 -
obs--96.44 %

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