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- PDB-8bem: STE20-like serine/threonine-protein kinase (SLK) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8bem
TitleSTE20-like serine/threonine-protein kinase (SLK) in complex with Tivozanib
ComponentsSTE20-like serine/threonine-protein kinase
KeywordsTRANSFERASE / Kinase / Typ II inhibitor / SLK / Tivozanib
Function / homology
Function and homology information


regulation of focal adhesion assembly / RHOB GTPase cycle / cell leading edge / RHOC GTPase cycle / 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 / cell leading edge / RHOC GTPase cycle / 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 / cytoplasm / cytosol
Similarity search - Function
Polo kinase kinase / Polo kinase kinase / UVR domain / UVR domain profile. / 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. ...Polo kinase kinase / Polo kinase kinase / UVR domain / UVR domain profile. / 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
Similarity search - Domain/homology
TIVOZANIB / STE20-like serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: STE20-like serine/threonine-protein kinase (SLK) in complex with Tivozanib
Authors: Kraemer, A. / Doelle, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: STE20-like serine/threonine-protein kinase
G: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,46511
Polymers138,3574
Non-polymers2,1087
Water54030
1
A: STE20-like serine/threonine-protein kinase
G: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2816
Polymers69,1792
Non-polymers1,1024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-34 kcal/mol
Surface area26220 Å2
MethodPISA
2
B: STE20-like serine/threonine-protein kinase
D: STE20-like serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1855
Polymers69,1792
Non-polymers1,0063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-26 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.012, 107.280, 129.400
Angle α, β, γ (deg.)90.000, 95.320, 90.000
Int Tables number4
Space group name H-MP1211

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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


Mass: 34589.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLK, KIAA0204, STK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2G2, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-AV9 / TIVOZANIB / 1-{2-chloro-4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}-3-[(3E)-5-methylisoxazol-3(2H)-ylidene]urea


Mass: 454.863 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19ClN4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350 0.2M Na2SO4 10% Ethylene Glycol 0.1M bis-tris propane 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000031 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.6→49.52 Å / Num. obs: 48206 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.054 / Rrim(I) all: 0.145 / Net I/σ(I): 11 / Num. measured all: 341607 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.697.31.0253229544360.7690.4051.1032.299.6
10.4-49.5270.04455857980.9990.0180.0473199

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.608
Highest resolutionLowest resolution
Rotation48.68 Å2.87 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0352refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HVD

6hvd


Resolution: 2.6→48.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2449 / WRfactor Rwork: 0.213 / FOM work R set: 0.7906 / SU B: 24.644 / SU ML: 0.244 / SU R Cruickshank DPI: 0.5243 / SU Rfree: 0.2927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.524 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2391 5 %RANDOM
Rwork0.2219 ---
obs0.2236 45795 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.71 Å2 / Biso mean: 53.733 Å2 / Biso min: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0.43 Å2
2--1.41 Å20 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 2.6→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8477 0 143 30 8650
Biso mean--58.86 39.48 -
Num. residues----1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168038
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.64112112
X-RAY DIFFRACTIONr_angle_other_deg0.4781.56318641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10251103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.705525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.293101393
X-RAY DIFFRACTIONr_chiral_restr0.0650.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021666
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 150 -
Rwork0.3 3412 -
all-3562 -
obs--99.58 %
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)
12.7202-0.8569-0.32952.43780.74111.50240.0604-0.3546-0.19330.4521-0.05810.15350.14840.017-0.00220.2476-0.0624-0.0580.06210.02610.05725.24449.7483-15.8138
22.65030.90010.82062.49660.49391.2955-0.01940.30510.2018-0.4-0.02090.3137-0.2682-0.12340.04030.25970.0529-0.09120.08970.01860.07191.769822.067-49.3197
32.48581.30530.7942.05950.68371.436-0.06780.0464-0.1519-0.08250.0053-0.13440.21540.09530.06250.20080.0492-0.05580.0595-0.04470.1017-5.4809-15.0204-49.8509
42.3652-1.4056-0.59463.01540.8732.3643-0.0105-0.01640.1558-0.0734-0.0572-0.2269-0.30090.1150.06770.2424-0.0537-0.10530.1058-0.03270.111817.306246.5646-14.0883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 309
2X-RAY DIFFRACTION2B17 - 310
3X-RAY DIFFRACTION3D17 - 310
4X-RAY DIFFRACTION4G17 - 309

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