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- PDB-4usf: Human SLK with SB-440719 -

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Basic information

Entry
Database: PDB / ID: 4usf
TitleHuman SLK with SB-440719
ComponentsSTE20-LIKE SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE
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 / regulation of apoptotic process / protein autophosphorylation / 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 / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / 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 / cytosol / cytoplasm
Similarity search - Function
Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Polo kinase kinase / : / Polo kinase kinase / UVR domain / UVR domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-6UI / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsElkins, J.M. / Salah, E. / Szklarz, M. / von Delft, F. / Bountra, C. / Edwards, A.M. / Knapp, S.
CitationJournal: Nat.Biotechnol. / Year: 2016
Title: Comprehensive Characterization of the Published Kinase Inhibitor Set.
Authors: Elkins, J.M. / Fedele, V. / Szklarz, M. / Abdul Azeez, K.R. / Salah, E. / Mikolajczyk, J. / Romanov, S. / Sepetov, N. / Huang, X.P. / Roth, B.L. / Al Haj Zen, A. / Fourches, D. / Muratov, E. ...Authors: Elkins, J.M. / Fedele, V. / Szklarz, M. / Abdul Azeez, K.R. / Salah, E. / Mikolajczyk, J. / Romanov, S. / Sepetov, N. / Huang, X.P. / Roth, B.L. / Al Haj Zen, A. / Fourches, D. / Muratov, E. / Tropsha, A. / Morris, J. / Teicher, B.A. / Kunkel, M. / Polley, E. / Lackey, K.E. / Atkinson, F.L. / Overington, J.P. / Bamborough, P. / Moller, S. / Price, D.J. / Willson, T.M. / Drewry, D.H. / Knapp, S. / Zuercher, W.J.
History
DepositionJul 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,9834
Polymers69,3812
Non-polymers6032
Water9,152508
1
A: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9922
Polymers34,6901
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9922
Polymers34,6901
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.940, 75.300, 189.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2188-

HOH

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Components

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


Mass: 34690.406 Da / Num. of mol.: 2 / 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-6UI / 4-[4-(6-methoxynaphthalen-2-yl)-1H-imidazol-5-yl]pyridine


Mass: 301.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6
Details: 20% PEG6000, 10% ETHYLENE GLYCOL, 0.1 M MES PH 6.0, 0.1 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorDate: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.75→48.4 Å / Num. obs: 72706 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.75→94.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.283 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22815 2839 4 %RANDOM
Rwork0.19685 ---
obs0.19812 68544 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.735 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.75→94.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 46 508 5002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194657
X-RAY DIFFRACTIONr_bond_other_d0.0040.024390
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9766347
X-RAY DIFFRACTIONr_angle_other_deg0.9913.00210143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92925.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63215802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5911514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215220
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021002
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.5782263
X-RAY DIFFRACTIONr_mcbond_other1.0611.5762262
X-RAY DIFFRACTIONr_mcangle_it1.8042.3542825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3271.7212394
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 185 -
Rwork0.301 5105 -
obs--99.12 %
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)
13.2269-1.1070.97481.5704-1.03811.19710.09410.1546-0.2288-0.1189-0.00250.19140.2057-0.1337-0.09160.0722-0.0242-0.00010.1171-0.04740.0661-18.8756-26.339923.7422
23.0263-0.29140.12121.9426-0.33452.60560.0610.47680.0963-0.2165-0.01330.0603-0.0273-0.0105-0.04760.03140.0052-0.00830.1707-0.02230.02560.5384-18.262610.3762
33.4005-0.67361.95750.6936-1.28572.64830.1083-0.2312-0.2057-0.11120.01470.08540.2672-0.1904-0.1230.0809-0.06150.02360.1377-0.07540.1168-9.44045.399251.5913
42.9324-0.5316-0.02291.46110.20642.43190.04270.3388-0.1039-0.1282-0.01540.11750.0946-0.1365-0.02730.01850.0014-0.02210.0751-0.04230.061410.09824.31436.3331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 110
2X-RAY DIFFRACTION2A111 - 400
3X-RAY DIFFRACTION3B1 - 110
4X-RAY DIFFRACTION4B111 - 400

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