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- PDB-2j51: Crystal structure of Human STE20-like kinase bound to 5-Amino-3-(... -

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Basic information

Entry
Database: PDB / ID: 2j51
TitleCrystal structure of Human STE20-like kinase bound to 5-Amino-3-((4-(aminosulfonyl)phenyl)amino) -N-(2,6-difluorophenyl)-1H-1,2,4-triazole- 1-carbothioamide
ComponentsSTE20-LIKE SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / MUSCLE DEVELOPMENT / KINASE / APOPTOSIS / GERMINAL CENTRE KINASE / SERINE/THREONINE KINASE 2 / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / protein autophosphorylation / regulation of apoptotic process / non-specific serine/threonine protein kinase ...regulation of focal adhesion assembly / RHOB GTPase cycle / RHOC GTPase cycle / cell leading edge / RHOA GTPase cycle / cytoplasmic microtubule organization / regulation of cell migration / protein autophosphorylation / regulation of apoptotic process / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-DKI / THIOCYANATE ION / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / Debreczeni, J.E. / von Delft, F. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / Debreczeni, J.E. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S.
CitationJournal: Embo J. / Year: 2008
Title: Activation Segment Dimerization: A Mechanism for Kinase Autophosphorylation of Non-Consensus Sites.
Authors: Pike, A.C.W. / Rellos, P. / Niesen, F.H. / Turnbull, A. / Oliver, A.W. / Parker, S.A. / Turk, B.E. / Pearl, L.H. / Knapp, S.
History
DepositionSep 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8947
Polymers37,1621
Non-polymers7326
Water2,720151
1
A: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules

A: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,78814
Polymers74,3242
Non-polymers1,46412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
MethodPQS
Unit cell
Length a, b, c (Å)101.195, 101.195, 177.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2105-

HOH

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Components

#1: Protein STE20-LIKE SERINE/THREONINE-PROTEIN KINASE / STE20-LIKE KINASE / STE20-RELATED SERINE/THREONINE-PROTEIN KINASE / STE20-RELATED KINASE / HSLK / ...STE20-LIKE KINASE / STE20-RELATED SERINE/THREONINE-PROTEIN KINASE / STE20-RELATED KINASE / HSLK / SERINE/THREONINE-PROTEIN KINASE 2 / CTCL TUMOR ANTIGEN SE20-9


Mass: 37162.070 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 19-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9H2G2, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYS 25 IS A CLONING ARTEFACT

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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: 3.53 Å3/Da / Density % sol: 65 %
Crystal growpH: 6.5
Details: 16% PEG3350, 0.15M KSCN, 10% ETG, 0.1M BTP PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→62.26 Å / Num. obs: 32094 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U5R

1u5r


Resolution: 2.1→60 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.058 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1589 5 %RANDOM
Rwork0.201 ---
obs0.202 30437 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 47 151 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222344
X-RAY DIFFRACTIONr_bond_other_d0.0030.021528
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9793188
X-RAY DIFFRACTIONr_angle_other_deg1.09533753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41525.588102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66315385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.391157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022588
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02443
X-RAY DIFFRACTIONr_nbd_refined0.2050.2468
X-RAY DIFFRACTIONr_nbd_other0.1880.21535
X-RAY DIFFRACTIONr_nbtor_refined0.170.21150
X-RAY DIFFRACTIONr_nbtor_other0.0870.21082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6251.51444
X-RAY DIFFRACTIONr_mcbond_other0.141.5572
X-RAY DIFFRACTIONr_mcangle_it1.14622334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7323900
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7954.5854
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: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 122 -
Rwork0.277 2198 -
obs--100 %
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)
19.6363-0.7194-0.17264.33640.14521.55370.11170.46280.6047-0.457-0.0501-0.1966-0.1849-0.3358-0.0616-0.2713-0.02840.11040.2532-0.2485-0.0239-42.583349.668-6.4292
23.9061-1.4361-0.31441.65250.78682.46430.1688-0.75930.3675-0.0275-0.11620.18970.1005-0.3547-0.0526-0.4073-0.13320.06480.1644-0.1318-0.2503-30.348638.2939-5.0208
34.37846.02790.990311.9810.37753.2790.3419-0.16810.31420.1494-0.0850.9918-0.0622-0.1389-0.2569-0.0080.05580.0125-0.31770.0314-0.1975-37.86084.7593-9.0046
43.38160.45720.49361.69331.16182.66040.1234-0.56440.22490.02140.1382-0.2650.16570.3423-0.2616-0.396-0.0880.01880.0068-0.0917-0.2836-13.671332.7164-9.3512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 70
2X-RAY DIFFRACTION2A71 - 188
3X-RAY DIFFRACTION3A189 - 207
4X-RAY DIFFRACTION4A208 - 308

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