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- PDB-8s3x: LIM Domain Kinase 2 (LIMK2) bound to compound 52 -

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Basic information

Entry
Database: PDB / ID: 8s3x
TitleLIM Domain Kinase 2 (LIMK2) bound to compound 52
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / Kinase / Inhibitor / Actin cytoskeleton
Function / homology
Function and homology information


cornea development in camera-type eye / head development / establishment of vesicle localization / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / mitotic spindle ...cornea development in camera-type eye / head development / establishment of vesicle localization / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / mitotic spindle / positive regulation of protein localization to nucleus / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
: / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Ple, K. / Knapp, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: LIM Domain Kinase 2 (LIMK2) bound to compound 52
Authors: Mathea, S. / Chatterjee, D. / Preuss, F. / Ple, K. / Knapp, S.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
#2: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIM domain kinase 2
B: LIM domain kinase 2
C: LIM domain kinase 2
D: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0618
Polymers139,1994
Non-polymers1,8624
Water23413
1
A: LIM domain kinase 2
C: LIM domain kinase 2
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 70.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,5314
Polymers69,5992
Non-polymers9312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-13 kcal/mol
Surface area22500 Å2
2
B: LIM domain kinase 2
D: LIM domain kinase 2
hetero molecules


  • defined by author
  • 70.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)70,5314
Polymers69,5992
Non-polymers9312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area22680 Å2
Unit cell
Length a, b, c (Å)86.911, 86.921, 103.297
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
LIM domain kinase 2 / LIMK-2


Mass: 34799.707 Da / Num. of mol.: 4 / Fragment: UNP residues 330-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-A1H41 / 4-(5-cyclopropyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-~{N}-[3-(3-methoxyphenyl)phenyl]-3,6-dihydro-2~{H}-pyridine-1-carboxamide


Mass: 465.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 16% PEG8000 0.04M potassium phosphate dibasic 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.59→45.83 Å / Num. obs: 47823 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.58 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.25
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.556 / Num. unique obs: 4734

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.9.8.1model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→45.83 Å / SU ML: 0.394 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.1049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2875 2380 4.99 %
Rwork0.2388 45337 -
obs0.2413 47717 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.77 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8006 0 140 13 8159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00578357
X-RAY DIFFRACTIONf_angle_d0.820811406
X-RAY DIFFRACTIONf_chiral_restr0.04971309
X-RAY DIFFRACTIONf_plane_restr0.00681565
X-RAY DIFFRACTIONf_dihedral_angle_d5.55911265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.640.42411630.34142651X-RAY DIFFRACTION99.5
2.64-2.70.38061430.31982656X-RAY DIFFRACTION99.64
2.7-2.760.35781500.32082594X-RAY DIFFRACTION99.71
2.76-2.830.32351360.31032672X-RAY DIFFRACTION99.79
2.83-2.910.42091300.3062659X-RAY DIFFRACTION99.64
2.91-2.990.37981510.29342680X-RAY DIFFRACTION99.61
2.99-3.090.34181190.27212647X-RAY DIFFRACTION99.57
3.09-3.20.28061420.25692673X-RAY DIFFRACTION99.68
3.2-3.330.31741340.27192680X-RAY DIFFRACTION99.79
3.33-3.480.30031170.25272676X-RAY DIFFRACTION99.64
3.48-3.660.311150.22552683X-RAY DIFFRACTION99.57
3.66-3.890.24331540.2232639X-RAY DIFFRACTION99.54
3.89-4.190.25211350.20642679X-RAY DIFFRACTION99.65
4.19-4.620.24111630.19822655X-RAY DIFFRACTION99.44
4.62-5.280.24481490.19582657X-RAY DIFFRACTION99.64
5.28-6.650.25281690.23372686X-RAY DIFFRACTION99.51
6.65-45.830.26471100.20382750X-RAY DIFFRACTION98.11
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)
11.249273901670.7635361251540.1576818418791.753069590731.681997364831.96891834740.3180047968710.0226133694435-0.01790340552940.273269085687-0.0214501231538-0.195784189601-0.4227925300090.0679440738324-0.243575193791.18716928111-0.1472381418060.1498831185220.367201888876-0.07863329264720.34294010320446.323444858847.656335695831.091249963
20.2194326841510.1632756045490.2403580350370.225742850647-0.02148459001970.632361054461-0.2963250433440.1796556845180.065838332723-0.03825718480310.254954200709-0.0296767811412-0.8509243209860.0468128140036-0.01738058607651.79521772174-0.1683135213950.2178164079450.470630185556-0.0434268166720.47557314562745.093682822362.802144124737.0048010835
32.68422762747-2.634237999320.1407068052333.44792780848-1.998223654264.77009917805-0.1910416415180.2395675488130.335523270193-0.2835870538680.2333762010240.166495940473-0.56087975952-0.0304852977905-0.03856792609750.678710085472-0.04591380536690.05857170431450.383191765238-0.004138299914680.302102539805-8.2764184437922.43540226526.4728658248
40.810836325635-0.00765336365389-0.8103413062750.635720700434-1.051681501812.558376141430.006234759609810.2240568308760.0356160391195-0.6080176444640.05438324022710.1593085225070.00601733102063-0.1797318676790.01378401883120.879471108807-0.005590141445210.01656648225390.3333087599140.02053438030110.279994080284-4.3546115649913.4509157492.58581464614
51.06860726986-0.363298497501-0.2780475588962.011743669850.5603584849692.98877196658-0.0263638877452-0.05165004140630.0469130670523-0.09975180973280.1030267685510.06965732989240.2632817347570.0185779378059-0.1108753678110.655924982871-0.006467263664950.0650921827220.318799846348-0.040512053920.2147275469642.523602241354.4897347755416.3077823863
60.917673360138-1.134351872220.09534032129622.06513370639-0.9762678870721.11615628616-0.244084184042-0.125815495525-0.2062679313020.02891524169210.190101077629-0.09198798946140.488820949934-0.108672342051-0.0454867245971.202265142120.06602188050760.0383675621580.3182903551080.03153940677290.2845809299283.54908431307-13.856945118514.7315537066
72.408353480850.7949554599452.364912058542.185645984811.153239711096.658633233530.04369289326490.4433058252380.503606764999-0.5519916774630.05595793795560.551251180176-0.7286897142270.02148127188070.05931787080880.3176889529670.2393942004110.005866669173740.3656765531150.1312155460980.4172722130232.295729080941.8836585242.12436676455
83.22820314225-0.859436081992-0.9883992996143.89966409168-2.573311056723.296656131490.117719231041-0.006981519783440.264728495361-0.40033417966-0.327039540263-0.22221151747-0.3497323062520.3272059453220.1764314012020.4647208131110.0972310087850.08225330386760.216115167015-0.002436390204730.23759025020444.370188499335.3890992867-2.31480212488
91.45016025316-0.7186361121910.1214044962934.56590472495-0.689305052084.03501390083-0.000853527532395-0.0599801535533-0.02124185429540.458166643077-0.03706885335970.0118018126724-0.0610220091411-0.09791477804540.001944459511380.276609300701-0.03161887133580.0595775305420.203010949331-0.02988519634520.22704427886542.241885878326.393406469314.7025303613
102.20464099855-1.15356032499-1.110150066364.973784269620.6310494381370.564930694737-0.152691846243-0.0801627021582-0.574166441315-0.159447057665.12170373544E-5-0.2969588253830.837275916445-0.07509508373340.01945989061810.8580942227280.0033367609315-0.00238195708750.2864991724780.02943447748420.41201600273248.124931811510.120039413315.9757782886
111.444758348430.0222927269812-1.210456939980.1344879688440.1285140061822.8475801105-0.141708877994-0.0324511671951-0.2291544567380.1410006791170.2132564271620.2243866988110.53998397229-0.3773113365270.09459985971771.07324329318-0.06082022200690.2818458204860.3636545867440.09162996451960.414949049838-14.52751399696.7436553837546.9595700358
120.1638576981140.121816164246-0.06718157808890.278505049027-0.5945115474151.525048098990.0119624494401-0.123980966432-0.01083489736110.4502443464840.1158587278180.07348062374260.0377606505226-0.123533242424-0.1364347017461.0499730351-0.04031724252440.150398167130.2923396292230.06375608012650.264831973714-7.8823536548315.295188236347.8350119109
130.2853803598790.173349527181-0.0238779896960.3694181631180.2210017808331.158587750280.05726448708160.1405237886740.01255487253050.2698894810430.223469673710.0809041757361-0.416584785264-0.03489905635860.2360958334921.13958457443-0.009092145889490.1894307040440.324938344876-0.06539276873370.09584376443330.064052206566726.974999772736.4918334889
141.497470237880.1574343649130.6845839338752.594829943082.0124412051.77414631274-0.2587188149870.180135407116-0.08180614338030.3739980398590.257251760211-0.228327637737-0.5690199333990.184312971494-0.0112765339171.21463357435-0.253591702130.07617323477580.402679807494-0.01218014919480.5913630732957.8408473805442.944179211631.3651096848
153.55949542668-2.18320079525-2.894530328623.149328497791.531071484856.35323755175-0.165276437361-0.39473517643-0.2525570398410.723530819128-0.01905586508070.7617335772390.447057457057-0.5564484308790.1894650462130.844270333036-0.1451771165910.3061101649950.456829162861-0.1441991456250.48235463213329.485713632527.214008436144.6122961137
160.3912709665590.340929133795-0.3210464798031.38122955160.3975209116260.671268975580.267563786655-0.09648318011460.07428076057591.00536488969-0.216021835673-0.00551151426734-0.239726812952-0.150338008306-0.100453421061.40056328548-0.06165317418420.2164304873150.43418581334-0.01776685824460.49079843147334.604100812636.345604879847.5571241421
170.292348706566-0.1751909757640.08893065665330.6127334142850.2404122620351.759206190270.198121288453-0.03161149940790.09196658689110.337442700155-0.11922249532-0.00239224909333-0.289860984977-0.08352489581670.1064313022751.36849728433-0.08828611207270.2503715828540.365059207392-0.04535745524130.31926535079639.395082364142.294902704941.0349475489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 513 through 593 )DD513 - 593147 - 227
22chain 'D' and (resid 594 through 631 )DD594 - 631228 - 263
33chain 'A' and (resid 334 through 366 )AA334 - 3661 - 27
44chain 'A' and (resid 367 through 424 )AA367 - 42428 - 82
55chain 'A' and (resid 425 through 593 )AA425 - 59383 - 230
66chain 'A' and (resid 594 through 631 )AA594 - 631231 - 268
77chain 'B' and (resid 330 through 366 )BB330 - 3661 - 37
88chain 'B' and (resid 367 through 397 )BB367 - 39738 - 68
99chain 'B' and (resid 398 through 575 )BB398 - 57569 - 220
1010chain 'B' and (resid 576 through 631 )BB576 - 631221 - 275
1111chain 'C' and (resid 330 through 366 )CC330 - 3661 - 37
1212chain 'C' and (resid 367 through 424 )CC367 - 42438 - 93
1313chain 'C' and (resid 425 through 616 )CC425 - 61694 - 258
1414chain 'C' and (resid 617 through 631 )CC617 - 631259 - 273
1515chain 'D' and (resid 331 through 366 )DD331 - 3661 - 28
1616chain 'D' and (resid 367 through 424 )DD367 - 42429 - 84
1717chain 'D' and (resid 425 through 512 )DD425 - 51285 - 146

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