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- PDB-5ote: MRCK beta in complex with BDP-00008900 -

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Basic information

Entry
Database: PDB / ID: 5ote
TitleMRCK beta in complex with BDP-00008900
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 / cell leading edge / RHOQ GTPase cycle / CDC42 GTPase cycle / cytoskeleton organization / small GTPase binding / cell-cell junction ...actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / RHOJ GTPase cycle / cell leading edge / RHOQ GTPase cycle / 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 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) 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 / CNH domain / Citron homology (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-AQE / Serine/threonine-protein kinase MRCK beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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)48,4744
Polymers48,0231
Non-polymers4513
Water2,918162
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)96,9498
Polymers96,0472
Non-polymers9026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6260 Å2
ΔGint-65 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.530, 44.300, 90.940
Angle α, β, γ (deg.)90.00, 106.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

CL

21A-711-

HOH

31A-760-

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-AQE / 2-[4-[(6~{S})-1,8-diazaspiro[5.5]undecan-8-yl]-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-1,3-thiazole


Mass: 353.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N5S
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / 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: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.68→29.41 Å / Num. obs: 49855 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.1
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia20.3.6.0data scaling
PDB_EXTRACT3.22data extraction
Coot0.7.2model building
XDS2013-03-30data reduction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAK

4uak


Resolution: 1.68→29.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.804 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2525 5.1 %RANDOM
Rwork0.196 ---
obs0.197 47317 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å21.13 Å2
2---3.54 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 1.68→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 30 162 3468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193340
X-RAY DIFFRACTIONr_bond_other_d00.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9644522
X-RAY DIFFRACTIONr_angle_other_deg3.6583.0057151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9815404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63824.076157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41715559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0771518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023757
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02778
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9381.3381625
X-RAY DIFFRACTIONr_mcbond_other1.9381.3381624
X-RAY DIFFRACTIONr_mcangle_it2.8921.9952026
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 187 -
Rwork0.272 3469 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: 19.067 Å / Origin y: 0.882 Å / Origin z: 18.827 Å
111213212223313233
T0.2312 Å2-0.021 Å2-0.105 Å2-0.3144 Å20.0022 Å2--0.0521 Å2
L2.0564 °2-0.3264 °21.1534 °2-0.2669 °2-0.1761 °2--1.1774 °2
S-0.0061 Å °-0.0973 Å °0.0101 Å °0.0599 Å °0.0266 Å °-0.0427 Å °-0.0382 Å °0.1186 Å °-0.0205 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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