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- PDB-5otf: MRCK beta in complex with BDP-00009066 -

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Basic information

Entry
Database: PDB / ID: 5otf
TitleMRCK beta in complex with BDP-00009066
ComponentsSerine/threonine-protein kinase MRCK beta
KeywordsCELL INVASION / MYOTONIC DYSTROPHY KINASE-RELATED CDC42-BINDING KINASE / METASTASIS / TRANSFERASE
Function / homology
Function and homology information


actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / cell leading edge / CDC42 GTPase cycle / cytoskeleton organization / small GTPase binding / cell-cell junction ...actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / cell leading edge / CDC42 GTPase cycle / cytoskeleton organization / small GTPase binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / magnesium ion binding / signal transduction / extracellular exosome / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase MRCK beta, catalytic domain / KELK-motif containing domain / KELK-motif containing domain of MRCK Ser/Thr protein kinase / Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / CRIB domain profile. ...Serine/threonine-protein kinase MRCK beta, catalytic domain / KELK-motif containing domain / KELK-motif containing domain of MRCK Ser/Thr protein kinase / Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 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
Chem-AQ5 / Serine/threonine-protein kinase MRCK beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchuettelkopf, A.W.
CitationJournal: Cancer Res. / Year: 2018
Title: Discovery of Potent and Selective MRCK Inhibitors with Therapeutic Effect on Skin Cancer.
Authors: Unbekandt, M. / Belshaw, S. / Bower, J. / Clarke, M. / Cordes, J. / Crighton, D. / Croft, D.R. / Drysdale, M.J. / Garnett, M.J. / Gill, K. / Gray, C. / Greenhalgh, D.A. / Hall, J.A.M. / ...Authors: Unbekandt, M. / Belshaw, S. / Bower, J. / Clarke, M. / Cordes, J. / Crighton, D. / Croft, D.R. / Drysdale, M.J. / Garnett, M.J. / Gill, K. / Gray, C. / Greenhalgh, D.A. / Hall, J.A.M. / Konczal, J. / Lilla, S. / McArthur, D. / McConnell, P. / McDonald, L. / McGarry, L. / McKinnon, H. / McMenemy, C. / Mezna, M. / Morrice, N.A. / Munro, J. / Naylor, G. / Rath, N. / Schuttelkopf, A.W. / Sime, M. / Olson, M.F.
History
DepositionAug 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MRCK beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5315
Polymers48,0231
Non-polymers5084
Water2,810156
1
A: Serine/threonine-protein kinase MRCK beta
hetero molecules

A: Serine/threonine-protein kinase MRCK beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,06310
Polymers96,0472
Non-polymers1,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6790 Å2
ΔGint-56 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.190, 44.056, 91.845
Angle α, β, γ (deg.)90.000, 107.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21A-706-

HOH

31A-756-

HOH

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Components

#1: Protein Serine/threonine-protein kinase MRCK beta / CDC42-binding protein kinase beta / CDC42BP-beta / DMPK-like beta / Myotonic dystrophy kinase- ...CDC42-binding protein kinase beta / CDC42BP-beta / DMPK-like beta / Myotonic dystrophy kinase-related CDC42-binding kinase beta / Myotonic dystrophy protein kinase-like beta


Mass: 48023.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42BPB, KIAA1124 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y5S2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AQ5 / (6~{S})-8-(3-pyrimidin-4-yl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,8-diazaspiro[5.5]undecane


Mass: 348.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.36 Å3/Da / Density % sol: 47.85 % / Mosaicity: 0.2 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: 12-18% PEG 3350, 100mM ammonium sulphate, 100mM sodium potassium tartrate, 100mM bis-tris pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.88 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2→29.77 Å / Num. obs: 29757 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.055 / Rrim(I) all: 0.102 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.30.856678920700.6420.551.0211.794.8
8.95-29.773.20.02211003450.9990.0150.02745.693.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
XDS2014-01-10data reduction
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAK

4uak


Resolution: 2→29.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.654 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1431 4.8 %RANDOM
Rwork0.1996 ---
obs0.201 28326 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.41 Å2 / Biso mean: 41.069 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.36 Å2
2---1.62 Å20 Å2
3---1.16 Å2
Refinement stepCycle: final / Resolution: 2→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 35 156 3499
Biso mean--34.5 41.16 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193378
X-RAY DIFFRACTIONr_bond_other_d00.023142
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9654573
X-RAY DIFFRACTIONr_angle_other_deg3.7523.0057228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3155409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35224.062160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71715564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4431519
X-RAY DIFFRACTIONr_chiral_restr0.140.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023804
X-RAY DIFFRACTIONr_gen_planes_other0.010.02786
X-RAY DIFFRACTIONr_mcbond_it1.621.9211642
X-RAY DIFFRACTIONr_mcbond_other1.621.9221641
X-RAY DIFFRACTIONr_mcangle_it2.5962.8692049
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 102 -
Rwork0.286 1961 -
all-2063 -
obs--94.89 %
Refinement TLS params.Method: refined / Origin x: 18.709 Å / Origin y: 1.099 Å / Origin z: 19.012 Å
111213212223313233
T0.1251 Å2-0.027 Å2-0.1113 Å2-0.2258 Å20.0022 Å2--0.1053 Å2
L2.0157 °2-0.483 °21.1039 °2-0.4454 °2-0.3252 °2--1.3855 °2
S-0.0264 Å °-0.1644 Å °0.0192 Å °0.1036 Å °0.0359 Å °-0.08 Å °-0.0679 Å °0.1701 Å °-0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 417
2X-RAY DIFFRACTION1L1 - 9999
3X-RAY DIFFRACTION1W1 - 9999
4X-RAY DIFFRACTION1X1 - 9999

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