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- PDB-2j7t: Crystal structure of human serine threonine kinase-10 bound to SU11274 -

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Basic information

Entry
Database: PDB / ID: 2j7t
TitleCrystal structure of human serine threonine kinase-10 bound to SU11274
ComponentsSERINE/THREONINE-PROTEIN KINASE 10
KeywordsTRANSFERASE / KINASE / ATP-BINDING / CELL CYCLE PROGRESSION / PHOSPHORYLATION / DISEASE MUTATION / NUCLEOTIDE- BINDING / LYMPHOCYTE ORIENTED KINASE (LOK) / SERINE/THREONINE- PROTEIN KINASE / SERINE/THREONINE KINASE (STK10A)
Function / homology
Function and homology information


lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear body / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / 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. ...Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / 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-274 / ACETATE ION / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Das, S. / Debreczeni, J. / Sobott, F. / Watt, S. / Savitsky, P. / Eswaran, J. / Turnbull, A.P. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Das, S. / Debreczeni, J. / Sobott, F. / Watt, S. / Savitsky, P. / Eswaran, J. / Turnbull, A.P. / Papagrigoriou, E. / Ugochukwa, E. / Gorrec, F. / Umeano, C.C. / von Delft, F. / Arrowsmith, C.H. / 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
DepositionOct 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,20610
Polymers34,2991
Non-polymers9089
Water2,342130
1
A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules

A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,41320
Polymers68,5972
Non-polymers1,81518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)49.192, 112.960, 133.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 10 / LYMPHOCYTE-ORIENTED KINASE / SERINE-THREONINE PROTEIN KINASE-10


Mass: 34298.605 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 18-317
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: O94804, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-274 / (3Z)-N-(3-CHLOROPHENYL)-3-({3,5-DIMETHYL-4-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-1H-PYRROL-2-YL}METHYLENE)-N-METHYL-2-OXOINDOLINE-5-SULFONAMIDE / MET KINASE INHIBITOR


Mass: 568.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30ClN5O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE DISCREPANCIES DUE TO CLONING ARTEFACTS

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 6.5
Details: 45% PEG300, 0.24M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→56.52 Å / Num. obs: 25648 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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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 2J51

2j51


Resolution: 2→55 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.399 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1308 5.1 %RANDOM
Rwork0.204 ---
obs0.205 24339 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--2.17 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 50 130 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222254
X-RAY DIFFRACTIONr_bond_other_d0.0010.021455
X-RAY DIFFRACTIONr_angle_refined_deg1.23623074
X-RAY DIFFRACTIONr_angle_other_deg1.3293.0023547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82224.82887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42515357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.418159
X-RAY DIFFRACTIONr_chiral_restr0.070.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_nbd_refined0.1970.2466
X-RAY DIFFRACTIONr_nbd_other0.1780.21500
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21101
X-RAY DIFFRACTIONr_nbtor_other0.0840.21093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5671.51463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87822276
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4133927
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2324.5798
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 113
Rwork0.261 1768
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)
13.1009-0.48030.46144.4656-1.25446.3464-0.01840.25180.8882-0.4543-0.0563-0.1357-1.8438-0.39460.07470.43330.21310.0273-0.18610.02280.0649-12.682445.070218.969
213.05720.163811.46423.44391.374715.1814-0.3818-1.31260.76710.43080.087-0.1915-0.46140.07190.2949-0.1795-0.0396-0.04080.10160.017-0.1831-33.430121.1705-2.5168
32.43710.16960.30481.39640.28615.24510.0410.1901-0.1331-0.0141-0.03770.04320.2289-0.3311-0.0033-0.28630.0293-0.0179-0.1979-0.0234-0.2407-11.327619.92719.1323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 114
2X-RAY DIFFRACTION2A193 - 212
3X-RAY DIFFRACTION3A115 - 188
4X-RAY DIFFRACTION3A213 - 317

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