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- PDB-5vda: Crystal structure of human WEE1 kinase domain in complex with RAC... -

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Basic information

Entry
Database: PDB / ID: 5vda
TitleCrystal structure of human WEE1 kinase domain in complex with RAC-IV-101, a MK1775 analogue
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE1 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis ...G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis / positive regulation of DNA replication / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / protein tyrosine kinase activity / cell division / nucleolus / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Wee1-like protein kinase / : / 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 ...Wee1-like protein kinase / : / 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-98D / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)UO1 HD076542 United States
CitationJournal: to be published
Title: Structural basis of Wee family kinase inhibition by small molecules
Authors: Zhu, J.-Y. / Schonbrunn, E.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0254
Polymers32,4411
Non-polymers5843
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.360, 44.640, 64.620
Angle α, β, γ (deg.)90.000, 102.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Wee1-like protein kinase / WEE1hu / Wee1A kinase


Mass: 32440.900 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P30291, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-98D / 1-{6-[(1S)-1-hydroxyethyl]pyridin-2-yl}-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one


Mass: 486.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N8O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-101

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 8, 2016 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→63.164 Å / Num. obs: 16522 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.647 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.051 / Χ2: 0.957 / Net I/σ(I): 20.66 / Num. measured all: 60253 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.6040.2645.0812140.9340.311100
2.15-2.213.6070.2086.3911640.9590.24499.4
2.21-2.283.6420.1936.7811530.9670.22799.5
2.28-2.353.6280.1647.9311280.9730.19299.6
2.35-2.423.6510.1389.310700.9830.16299.4
2.42-2.513.6540.1210.3610780.9870.14199.7
2.51-2.63.6630.11511.2510090.9880.135100
2.6-2.713.6880.09113.59670.9920.10799.4
2.71-2.833.6880.07415.959460.9950.08799.8
2.83-2.973.6650.06418.659050.9960.07599.5
2.97-3.133.7080.04923.118350.9970.057100
3.13-3.323.6960.03928.998200.9980.04699.4
3.32-3.553.6950.03134.47600.9990.03699.3
3.55-3.833.6610.02542.127070.9990.02998.9
3.83-4.23.6730.02445.126540.9990.02999.8
4.2-4.73.6390.02149.695900.9990.02599
4.7-5.423.630.02147.555300.9990.02599.6
5.42-6.643.6080.02345.794570.9990.02798.9
6.64-9.393.5590.0253.763450.9990.02496.9
9.39-63.1643.1680.01958.161900.9990.02390.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→63.164 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2554 827 5.01 %
Rwork0.1906 --
obs-16520 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 245.6 Å2 / Biso mean: 46.0356 Å2 / Biso min: 13.46 Å2
Refinement stepCycle: final / Resolution: 2.1→63.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 77 83 2221
Biso mean--35.67 31.85 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142148
X-RAY DIFFRACTIONf_angle_d1.5982900
X-RAY DIFFRACTIONf_chiral_restr0.058312
X-RAY DIFFRACTIONf_plane_restr0.008371
X-RAY DIFFRACTIONf_dihedral_angle_d15.082806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.23160.2871370.223825942731100
2.2316-2.40390.28531360.216925912727100
2.4039-2.64580.31721380.219826082746100
2.6458-3.02860.26891370.214926102747100
3.0286-3.81570.24471380.17762624276299
3.8157-63.1930.23431410.16632666280798
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)
15.5732-2.1982-1.22813.45791.22923.69440.05720.1695-0.3759-0.3261-0.06640.20970.1832-0.2353-0.04740.29610.0142-0.03890.22410.09590.2801-11.6392-2.22047.6594
21.9731-1.09020.0282.65651.32561.82530.0657-0.4022-0.4919-0.31510.20720.14390.17820.21190.33690.3651-0.015-0.03060.27520.13690.38-7.268-6.62159.3866
34.106-0.23650.8653.52160.84390.89290.41950.5202-1.0112-0.81870.41140.7695-0.0445-0.58621.04840.5777-0.0031-0.11830.19990.06080.71176.0841-9.228913.3017
43.8728-0.36741.01552.5059-1.3232.6103-0.2503-0.38760.23060.23080.15030.0844-0.4366-0.1689-0.12650.30820.05860.02060.1910.00770.1259-0.30696.672318.153
54.0260.10871.51893.6853-1.33264.740.12950.2753-0.4301-0.118-0.1135-0.33160.18490.287-0.02770.24130.00490.01280.17830.04060.23078.59872.702515.8614
65.1904-1.47580.83713.5933-0.35491.9103-0.3235-0.11261.07260.3462-0.1034-1.0261-0.34910.3583-0.25030.3647-0.0518-0.14240.28430.07260.572217.945413.723718.7696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 318 )A293 - 318
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 337 )A319 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 353 )A338 - 353
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 420 )A354 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 484 )A421 - 484
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 571 )A485 - 571

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