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- PDB-4ual: MRCK beta in complex with BDP00005290 -

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Basic information

Entry
Database: PDB / ID: 4ual
TitleMRCK beta in complex with BDP00005290
ComponentsSerine/threonine-protein kinase MRCK beta
KeywordsTRANSFERASE / myotonic dystrophy kinase-related CDC42-binding kinase / metastasis / cell invasion
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-3FV / Serine/threonine-protein kinase MRCK beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSchuettelkopf, A.W.
CitationJournal: Cell Commun. Signal / Year: 2014
Title: A novel small-molecule MRCK inhibitor blocks cancer cell invasion.
Authors: Unbekandt, M. / Croft, D.R. / Crighton, D. / Mezna, M. / McArthur, D. / McConnell, P. / Schuttelkopf, A.W. / Belshaw, S. / Pannifer, A. / Sime, M. / Bower, J. / Drysdale, M. / Olson, M.F.
History
DepositionAug 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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

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)48,5285
Polymers48,0231
Non-polymers5054
Water3,513195
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)97,05610
Polymers96,0472
Non-polymers1,0108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6700 Å2
ΔGint-103 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.030, 44.030, 91.120
Angle α, β, γ (deg.)90.00, 107.27, 90.00
Int Tables number5
Space group name H-MC121

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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-3FV / 4-chloro-1-(piperidin-4-yl)-N-[3-(pyridin-2-yl)-1H-pyrazol-4-yl]-1H-pyrazole-3-carboxamide


Mass: 371.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18ClN7O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
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
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.71→43.51 Å / Num. all: 46470 / Num. obs: 46470 / % possible obs: 98 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.7
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TKU

3tku


Resolution: 1.71→43.51 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 2350 5.06 %
Rwork0.2047 --
obs0.2063 46468 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 32 195 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173372
X-RAY DIFFRACTIONf_angle_d1.6864556
X-RAY DIFFRACTIONf_dihedral_angle_d14.4461257
X-RAY DIFFRACTIONf_chiral_restr0.088488
X-RAY DIFFRACTIONf_plane_restr0.009586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.74490.34321400.28582580X-RAY DIFFRACTION99
1.7449-1.78290.3111220.26392562X-RAY DIFFRACTION98
1.7829-1.82430.28631480.24782613X-RAY DIFFRACTION99
1.8243-1.870.3041440.24222579X-RAY DIFFRACTION99
1.87-1.92050.29911370.23492617X-RAY DIFFRACTION98
1.9205-1.9770.29711240.23162577X-RAY DIFFRACTION99
1.977-2.04080.26941460.22092552X-RAY DIFFRACTION97
2.0408-2.11380.2511510.21852569X-RAY DIFFRACTION97
2.1138-2.19840.28161480.22642581X-RAY DIFFRACTION98
2.1984-2.29850.27931150.23172596X-RAY DIFFRACTION97
2.2985-2.41960.29551390.23142536X-RAY DIFFRACTION97
2.4196-2.57120.26631450.2362563X-RAY DIFFRACTION96
2.5712-2.76970.29561250.24322555X-RAY DIFFRACTION96
2.7697-3.04840.24441270.21992588X-RAY DIFFRACTION97
3.0484-3.48930.21321630.19372635X-RAY DIFFRACTION99
3.4893-4.39550.17311290.15562702X-RAY DIFFRACTION99
4.3955-43.52010.19641470.17832713X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08740.20730.39460.5011-0.37522.19970.0238-0.20130.02620.1725-0.01340.0402-0.13820.0238-0.00930.163-0.0320.00460.08730.01750.12530.02924.34238.1204
22.7684-0.61411.38650.567-0.25880.8704-0.07440.12480.07490.02470.0513-0.0685-0.09010.20870.01930.2419-0.0603-0.01170.23880.01160.106628.78660.409223.583
32.0162-0.57710.78920.8057-0.80721.08090.0252-0.4811-0.30640.3680.05470.0028-0.0479-0.1417-0.05590.3332-0.0412-0.04560.19870.06180.17912.5124-3.357420.0875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION3chain 'A' and (resid 343 through 417 )A343 - 417
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 342 )A101 - 342
3X-RAY DIFFRACTION1chain 'A' and (resid -1 through 100A-1 - 100

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