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- PDB-7ats: The LIMK1 Kinase Domain Bound To LIJTF500127 -

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Basic information

Entry
Database: PDB / ID: 7ats
TitleThe LIMK1 Kinase Domain Bound To LIJTF500127
ComponentsLIM domain kinase 1
KeywordsSIGNALING PROTEIN / Kinase Inhibitor Active site CFL1 Actin cytoskeleton
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / positive regulation of axon extension / heat shock protein binding / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / postsynapse / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / neuron projection / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / glutamatergic synapse / signal transduction / ATP binding / membrane / nucleus / metal ion binding / cytosol / 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 ...: / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-RXQ / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Yamamoto, S. / Tawada, M. / Nomura, I. / Takagi, T. / Ahmed, M. / Little, W. / Mueller-Knapp, S. / Knapp, S.
CitationJournal: To Be Published
Title: The LIMK1 Kinase Domain Bound To LIJTF500127
Authors: Mathea, S. / Chatterjee, D. / Preuss, F. / Yamamoto, S. / Tawada, M. / Nomura, I. / Takagi, T. / Ahmed, M. / Little, W. / Mueller-Knapp, S. / Knapp, S.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5192
Polymers35,9951
Non-polymers5241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)81.096, 81.096, 173.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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


Mass: 35994.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RXQ / N-[3-[5-(4-Chlorophenyl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl]benzenesulfonamide / N-[3-[[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl]-2,4-bis(fluoranyl)phenyl]benzenesulfonamide / LIJTF500127


Mass: 523.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H16ClF2N3O3S / Feature type: SUBJECT OF INVESTIGATION
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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 0.1 M bis-tris-propane pH 7.5 0.2 M potassium thiocyanate 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→44.71 Å / Num. obs: 8956 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 94.95 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.5
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1255

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Processing

Software
NameVersionClassification
REFMAC7.0.053refinement
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NXC

5nxc


Resolution: 2.8→44.71 Å / SU ML: 0.2732 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 38.678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3122 449 5.04 %
Rwork0.2478 8454 -
obs0.2511 8903 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 36 0 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141975
X-RAY DIFFRACTIONf_angle_d1.34262718
X-RAY DIFFRACTIONf_chiral_restr0.0699309
X-RAY DIFFRACTIONf_plane_restr0.0093390
X-RAY DIFFRACTIONf_dihedral_angle_d7.4702319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.34681520.27332717X-RAY DIFFRACTION99.97
3.21-4.040.32581440.27262774X-RAY DIFFRACTION99.93
4.04-44.710.3021530.23512963X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -12.2841886409 Å / Origin y: 32.145028667 Å / Origin z: -7.88985935969 Å
111213212223313233
T0.635629711395 Å2-0.0281263147259 Å2-0.0270613761225 Å2-0.693957867867 Å2-0.017309484848 Å2--0.579963937761 Å2
L1.63731232605 °20.880219880356 °2-0.305160095579 °2-1.17013150677 °20.45108340405 °2--0.588301841079 °2
S0.056830386854 Å °0.171652045231 Å °-0.20553232865 Å °-0.0629114457101 Å °0.0424772208982 Å °0.00431980323005 Å °0.0522710041761 Å °0.118832730826 Å °0.000189370033369 Å °
Refinement TLS groupSelection details: all

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