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- PDB-5vc6: crystal structure of human WEE1 kinase domain in complex with PHA... -

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Basic information

Entry
Database: PDB / ID: 5vc6
Titlecrystal structure of human WEE1 kinase domain in complex with PHA-848125
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 / phosphorylation / 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 / Protein kinase, ATP binding site ...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-P48 / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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: J. Med. Chem. / Year: 2017
Title: Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Authors: Zhu, J.Y. / Cuellar, R.A. / Berndt, N. / Lee, H.E. / Olesen, S.H. / Martin, M.P. / Jensen, J.T. / Georg, G.I. / Schonbrunn, E.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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)32,9643
Polymers32,4411
Non-polymers5232
Water1,69394
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)50.430, 44.920, 64.800
Angle α, β, γ (deg.)90.000, 102.910, 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-P48 / N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE


Mass: 460.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N8O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
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 PHA-848125

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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: Nov 10, 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→63.163 Å / Num. obs: 18665 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.716 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 0.935 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.7470.2655.6213780.9060.30995.3
2.05-2.113.7350.226.6312990.9310.25794.5
2.11-2.173.7560.1698.0912720.9530.19795.9
2.17-2.243.7440.1489.2212680.9710.17396.4
2.24-2.313.7630.1379.8412180.9750.1695.1
2.31-2.393.7540.1111.9311850.9860.12896.7
2.39-2.483.7480.09513.2811370.9890.11197.1
2.48-2.583.7580.08814.1411230.990.10396.6
2.58-2.73.7420.06917.3910460.9950.08196.4
2.7-2.833.7590.06319.0810300.9950.07395.9
2.83-2.983.7490.05722.569520.9950.06696.3
2.98-3.163.7420.04426.969180.9960.05197.3
3.16-3.383.6970.03731.578740.9970.04398.1
3.38-3.653.6620.029378070.9980.03498.3
3.65-43.6530.02841.557520.9980.03397.4
4-4.473.6210.02444.856880.9990.02998.6
4.47-5.163.6150.02345.725950.9990.02796.1
5.16-6.323.5810.02543.15180.9980.02997.4
6.32-8.943.5150.02446.174020.9990.02897.6
8.94-63.1633.310.02248.362030.9990.02684.2

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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
Starting model: 5V5Y

5v5y


Resolution: 2→63.163 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.41
RfactorNum. reflection% reflection
Rfree0.2645 934 5 %
Rwork0.22 --
obs-18663 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.76 Å2 / Biso mean: 37.6689 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 2→63.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 76 94 2231
Biso mean--31.89 28.55 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072146
X-RAY DIFFRACTIONf_angle_d1.0142900
X-RAY DIFFRACTIONf_chiral_restr0.042311
X-RAY DIFFRACTIONf_plane_restr0.005372
X-RAY DIFFRACTIONf_dihedral_angle_d14.555804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9999-2.10540.30221310.25152490262195
2.1054-2.23730.26991310.23892489262096
2.2373-2.410.29541330.24172513264696
2.41-2.65260.30411320.24542522265497
2.6526-3.03640.28481340.23812541267597
3.0364-3.82550.24151360.20622578271498
3.8255-63.1940.24841370.19412596273396
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)
12.8444-1.43470.81461.39590.77442.2844-0.0445-0.124-0.4432-0.20090.03920.14680.24410.21520.00540.28290.00280.01730.26580.10930.289540.3654-3.76878.4179
25.1001-1.82010.49054.19080.69813.24480.89770.5677-0.8106-0.74-0.06980.4648-0.4121-0.11082.03120.46530.027-0.09880.19330.0290.575756.4569-9.26312.4383
33.315-0.24281.43122.1145-0.62152.4795-0.1811-0.47250.12510.1820.0944-0.0051-0.1816-0.0616-0.08820.22810.0270.0160.20610.05340.098950.71736.720318.218
45.49742.6539-0.0011.5949-0.94312.8341-0.21310.7268-0.9124-0.44710.0144-0.55440.4438-0.03660.03070.3139-0.01790.05990.32720.04160.318563.9642-0.525713.3763
53.4178-0.40030.07222.50970.0471.9438-0.2058-0.11850.89010.3784-0.1422-0.7625-0.44210.4392-0.83580.3605-0.0451-0.12220.24180.04460.4268.130914.077118.7489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 337 )A293 - 337
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 352 )A338 - 352
3X-RAY DIFFRACTION3chain 'A' and (resid 353 through 461 )A353 - 461
4X-RAY DIFFRACTION4chain 'A' and (resid 462 through 484 )A462 - 484
5X-RAY DIFFRACTION5chain 'A' and (resid 485 through 571 )A485 - 571

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