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- PDB-2jfl: CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (DIPHOSPHORYLATED FO... -

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Basic information

Entry
Database: PDB / ID: 2jfl
TitleCRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (DIPHOSPHORYLATED FORM) 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 / SERINE-THREONINE-PROTEIN KINASE
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: 2.2 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / von Delft, F. / Arrowsmith, C.H. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / 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
DepositionFeb 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1519
Polymers37,3221
Non-polymers8298
Water2,630146
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)76,30318
Polymers74,6442
Non-polymers1,65916
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)101.368, 101.368, 177.238
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-2101-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37322.031 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

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Non-polymers , 5 types, 154 molecules

#2: 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsK25T MUTATION DUE TO CLONING ARTIFACT

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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: 65.1 %
Crystal growpH: 6.5
Details: 18% PEG3350,10% ETHYLENE GLYCOL, 0.15 KSCN, 0.1M BISTRIS PROPANE PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97945
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 27969 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J51

2j51


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.975 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHOSPHO GROUPS ON THR183 AND SER189 HAVE BEEN MODELLED WITH OCCUPANCIES OF 0.7 AND 0.3 RESPECTIVELY. MASS SPEC INDICATES RATIO OF MONO-TO- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHOSPHO GROUPS ON THR183 AND SER189 HAVE BEEN MODELLED WITH OCCUPANCIES OF 0.7 AND 0.3 RESPECTIVELY. MASS SPEC INDICATES RATIO OF MONO-TO-DI PHOSPHORYLATION IS 70- 30
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1377 4.9 %RANDOM
Rwork0.203 ---
obs0.205 26523 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 52 146 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222371
X-RAY DIFFRACTIONr_bond_other_d0.0030.021567
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9863222
X-RAY DIFFRACTIONr_angle_other_deg1.1563.0013833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64125.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23915.038395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022598
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02451
X-RAY DIFFRACTIONr_nbd_refined0.1950.2452
X-RAY DIFFRACTIONr_nbd_other0.1920.21572
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21137
X-RAY DIFFRACTIONr_nbtor_other0.0930.21119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.51444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95822337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5943927
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4814.5885
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→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 74 -
Rwork0.306 1840 -
obs--94.57 %
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)
111.4561-0.95521.0134.84880.58395.29940.22360.40980.7266-0.662-0.1031-0.2826-0.3919-0.0883-0.1206-0.3343-0.010.12830.305-0.2040.0382-42.36549.883-6.553
24.197-1.5163-0.34021.72270.512.50460.1426-0.73170.3173-0.0408-0.09910.19650.1553-0.2844-0.0436-0.3694-0.12460.05260.2382-0.0927-0.2074-30.58737.727-5.214
35.38117.18791.096914.89851.28546.14880.4846-0.36060.63540.3464-0.22830.8836-0.20130.0224-0.2563-0.03420.07150.0259-0.36770.0482-0.1999-37.9194.694-8.989
43.83020.75160.45452.32071.12823.50230.0918-0.6120.15370.11040.1282-0.26380.16690.3824-0.22-0.3966-0.07130.0180.086-0.0672-0.229-13.59232.767-9.389
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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