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- PDB-7atu: The LIMK1 Kinase Domain Bound To LIJTF500025 -

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Basic information

Entry
Database: PDB / ID: 7atu
TitleThe LIMK1 Kinase Domain Bound To LIJTF500025
ComponentsLIM domain kinase 1
KeywordsSIGNALING PROTEIN / Kinase Inhibitor 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 / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / nuclear speck / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / metal ion binding / nucleus / 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 / 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
Chem-RXN / 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 LIJTF500025
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 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.formula / _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: LIM domain kinase 1
B: LIM domain kinase 1
C: LIM domain kinase 1
D: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8998
Polymers143,9794
Non-polymers1,9204
Water905
1
A: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4752
Polymers35,9951
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
B: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4752
Polymers35,9951
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
3
C: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4752
Polymers35,9951
Non-polymers4801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
4
D: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4752
Polymers35,9951
Non-polymers4801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)85.234, 83.838, 98.029
Angle α, β, γ (deg.)90.000, 92.339, 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 1 / LIMK-1


Mass: 35994.773 Da / Num. of mol.: 4
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-RXN / (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide / 6-[(3S)-8-chloranyl-5-methyl-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-7-oxidanylidene-2-(phenylmethyl)-4,5-dihydropyrazolo[3,4-c]pyridine-3-carboxamide / LIJTF500025


Mass: 479.916 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H22ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citrate pH 5.9 0.2 M NaCl 8% jeffamine M-600 0.005 M iron chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→48.97 Å / Num. obs: 33787 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.32 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.94 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4516

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Processing

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

5nxc


Resolution: 2.8→43.22 Å / SU ML: 0.4892 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 34.7301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3159 1719 5.09 %
Rwork0.2401 32043 -
obs0.2438 33762 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 136 5 7875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018089
X-RAY DIFFRACTIONf_angle_d1.22211054
X-RAY DIFFRACTIONf_chiral_restr0.06541227
X-RAY DIFFRACTIONf_plane_restr0.00841519
X-RAY DIFFRACTIONf_dihedral_angle_d17.61611240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.38241320.31382714X-RAY DIFFRACTION99.68
2.88-2.980.32611490.30392653X-RAY DIFFRACTION99.68
2.98-3.080.42171340.29872674X-RAY DIFFRACTION99.15
3.08-3.210.34451230.2642659X-RAY DIFFRACTION99.14
3.21-3.350.34091500.24962675X-RAY DIFFRACTION99.33
3.35-3.530.33161460.24982672X-RAY DIFFRACTION98.57
3.53-3.750.37171240.30862474X-RAY DIFFRACTION91.67
3.75-4.040.30381710.21082672X-RAY DIFFRACTION99.86
4.04-4.440.27451690.18222689X-RAY DIFFRACTION99.83
4.44-5.090.2671180.18732725X-RAY DIFFRACTION99.75
5.09-6.40.33171450.24032701X-RAY DIFFRACTION99.06
6.4-43.220.29171580.25722735X-RAY DIFFRACTION98.33

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