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- PDB-2uv2: Crystal Structure Of Human Ste20-Like Kinase Bound To 4-(4-(5- Cy... -

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Basic information

Entry
Database: PDB / ID: 2uv2
TitleCrystal Structure Of Human Ste20-Like Kinase Bound To 4-(4-(5- Cyclopropyl-1H-pyrazol-3-ylamino)-quinazolin-2-ylamino)-phenyl)- acetonitrile
ComponentsSTE20-LIKE SERINE-THREONINE 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-GVD / THIOCYANATE ION / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / Debreczeni, J.E. / von Delft, F. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Keates, T. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Bunkoczi, G. / Debreczeni, J.E. / 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
DepositionMar 8, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionMar 20, 2007ID: 2JA0
Revision 1.0Mar 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,9709
Polymers37,1621
Non-polymers8088
Water2,666148
1
A: STE20-LIKE SERINE-THREONINE KINASE
hetero molecules

A: STE20-LIKE SERINE-THREONINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,94018
Polymers74,3242
Non-polymers1,61616
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)101.260, 101.260, 176.471
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-2106-

HOH

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Components

#1: Protein STE20-LIKE SERINE-THREONINE 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 / Mutation: YES
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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-GVD / [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE


Mass: 381.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 25 TO THR
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 %
Crystal growpH: 6.5
Details: 18% PEG3350, 0.15M POTASSIUM THIOCYANATE, 10% ETHYLENE GLYCOL, 0.1M BISTRISPROPANE PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9687
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. obs: 24390 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 95.2

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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: 2.3→60 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.504 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1232 5.1 %RANDOM
Rwork0.198 ---
obs0.199 23095 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 55 148 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222350
X-RAY DIFFRACTIONr_bond_other_d0.0020.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9833191
X-RAY DIFFRACTIONr_angle_other_deg0.9533.0033763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71225.437103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.1790.2445
X-RAY DIFFRACTIONr_nbd_other0.1840.21500
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21130
X-RAY DIFFRACTIONr_nbtor_other0.0890.21126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.51498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84822323
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.25731019
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8564.5865
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 87 -
Rwork0.289 1523 -
obs--90.86 %
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)
113.82130.2351.9194.60771.82875.15720.15720.80130.3787-0.6277-0.0188-0.2475-0.3251-0.2036-0.1383-0.29580.00090.12130.305-0.24590.0893-43.05449.576-6.328
24.3683-1.77460.17021.55330.68883.11080.1669-0.74040.41810.0455-0.1690.22170.1578-0.38610.002-0.4247-0.11790.070.157-0.1628-0.2197-30.28938.19-4.942
36.34925.79172.315514.28971.97687.60830.3431-0.37490.81220.4737-0.14421.0316-0.3840.2226-0.199-0.25280.07510.0119-0.6410.0516-0.5046-37.8544.71-9.042
44.38970.48230.70542.26411.3314.0810.1085-0.65250.22180.07850.1484-0.29180.17980.3415-0.2569-0.479-0.08190.0263-0.095-0.1114-0.3418-13.68532.675-9.196
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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