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- PDB-4tpt: Crystal Structure of the Human LIMK2 Kinase Domain In Complex Wit... -

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Basic information

Entry
Database: PDB / ID: 4tpt
TitleCrystal Structure of the Human LIMK2 Kinase Domain In Complex With a Non-ATP Competitive Inhibitor
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / LIMK2 KINASE / DFG INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-35H / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGoodwin, N.C. / Cianchetta, G. / Hamman, B.L. / Burgoon, H.A. / Healy, J. / Mabon, S. / Strobel, E.D. / Wang, S. / Rawlins, D.B.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Discovery of a Type III Inhibitor of LIM Kinase 2 That Binds in a DFG-Out Conformation.
Authors: Goodwin, N.C. / Cianchetta, G. / Burgoon, H.A. / Healy, J. / Mabon, R. / Strobel, E.D. / Allen, J. / Wang, S. / Hamman, B.D. / Rawlins, D.B.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 2.0Dec 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / chem_comp_atom ...atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0444
Polymers69,1632
Non-polymers8812
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-26 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.569, 77.903, 86.387
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34581.434 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 330-632)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Production host: unidentified baculovirus
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-35H / N-{4-[(1S)-1,2-dihydroxyethyl]benzyl}-N-methyl-4-(phenylsulfamoyl)benzamide


Mass: 440.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C23H24N2O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: batch mode
Details: The purified protein was used in crystallisation trials employing both, a standard screen with approximately 1200 different conditions, as well as crystallisation conditions identified using literature data.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→84.82 Å / Num. obs: 20794 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 0
Reflection shellResolution: 2.6→2.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.724 / % possible all: 87.8

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→84.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 29.863 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 1.063 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27413 919 4.5 %RANDOM
Rwork0.22046 ---
obs0.22294 19409 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.389 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-2.53 Å2
2---2.08 Å20 Å2
3---2.03 Å2
Refinement stepCycle: 1 / Resolution: 2.6→84.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 62 30 4509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224589
X-RAY DIFFRACTIONr_bond_other_d0.0010.024242
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.9966209
X-RAY DIFFRACTIONr_angle_other_deg0.71939891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88824.18189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24415811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8121519
X-RAY DIFFRACTIONr_chiral_restr0.0560.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02924
X-RAY DIFFRACTIONr_nbd_refined0.20.2973
X-RAY DIFFRACTIONr_nbd_other0.1590.24150
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22270
X-RAY DIFFRACTIONr_nbtor_other0.0780.22442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1240.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04823636
X-RAY DIFFRACTIONr_mcbond_other0.17421124
X-RAY DIFFRACTIONr_mcangle_it1.33834484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89542158
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.80361725
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: 2.6→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 53 -
Rwork0.364 1176 -
obs--80.59 %
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)
13.85661.05091.41652.77470.6173.07820.05580.1642-0.57890.05160.1505-0.37020.33780.4819-0.2063-0.00520.0790.0298-0.0152-0.04970.11915.571-9.09117.955
21.92831.2251.22133.35440.97742.1963-0.08820.15350.2281-0.25910.09120.2754-0.2612-0.1314-0.0031-0.09440.03670.04240.02940.00920.0172-1.1148.70911.898
32.78060.39620.66343.9025-0.04244.2382-0.0209-0.3753-0.03930.661-0.04370.1426-0.1343-0.36850.06460.13720.03660.08340.0639-0.0579-0.09146.27112.0441.523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A340 - 407
2X-RAY DIFFRACTION1B330 - 339
3X-RAY DIFFRACTION2A408 - 631
4X-RAY DIFFRACTION2B340 - 407
5X-RAY DIFFRACTION2A330 - 339
6X-RAY DIFFRACTION3B408 - 632

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