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- PDB-5vdk: Crystal structure of human WEE2 kinase domain in complex with MK1775 -

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Basic information

Entry
Database: PDB / ID: 5vdk
TitleCrystal structure of human WEE2 kinase domain in complex with MK1775
ComponentsWee1-like protein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE2 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


female pronucleus assembly / regulation of meiosis I / negative regulation of oocyte maturation / regulation of fertilization / female meiotic nuclear division / positive regulation of phosphorylation / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / mitotic cell cycle / protein tyrosine kinase activity ...female pronucleus assembly / regulation of meiosis I / negative regulation of oocyte maturation / regulation of fertilization / female meiotic nuclear division / positive regulation of phosphorylation / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / mitotic cell cycle / protein tyrosine kinase activity / magnesium ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Wee1-like protein kinase / : / 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 ...Wee1-like protein kinase / : / 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-8X7 / PHOSPHATE ION / Wee1-like protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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
DepositionApr 3, 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 / 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8575
Polymers33,0711
Non-polymers7864
Water1267
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)68.810, 68.810, 58.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Wee1-like protein kinase 2 / Wee1-like protein kinase 1B / Wee1B kinase


Mass: 33071.246 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 202-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE2, WEE1B / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P0C1S8, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-8X7 / 1-[6-(2-hydroxypropan-2-yl)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: 500.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32N8O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14 MG/ML WEE2, 25 mM TRIS PH 8.0, 1 mM DTT, 0.2 M ammonium phosphate monobasic, 1.5 mM MK1775

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 14, 2015 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→18.794 Å / Num. obs: 8422 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.374 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.109 / Χ2: 1.006 / Net I/σ(I): 12.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.774.4390.573.46400.8290.646100
2.77-2.854.4480.4354.415910.8830.493100
2.85-2.934.4250.3425.096020.920.38999.8
2.93-3.024.4540.2886.165590.9410.327100
3.02-3.124.4610.2357.455660.9450.267100
3.12-3.234.420.1739.115530.9710.197100
3.23-3.354.4350.14510.475130.9760.165100
3.35-3.494.4210.11812.265030.9860.133100
3.49-3.644.3430.09614.294950.9910.109100
3.64-3.824.3570.08415.774450.990.095100
3.82-4.034.2870.07417.744210.9910.084100
4.03-4.274.280.07218.324290.990.081100
4.27-4.564.2350.06419.853910.9910.072100
4.56-4.934.2580.06319.823610.9940.071100
4.93-5.44.3480.06519.213190.9940.073100
5.4-6.044.370.06519.633030.9920.073100
6.04-6.974.3090.06320.342690.9950.071100
6.97-8.544.2430.05921.492180.9930.067100
8.54-12.084.180.05523.231720.9960.06199.4
12.08-18.7944.3190.05123.85720.9930.05775.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X8B

1x8b


Resolution: 2.7→18.794 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.37
RfactorNum. reflection% reflection
Rfree0.2843 422 5.01 %
Rwork0.2253 --
obs0.2281 8421 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→18.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 52 7 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032143
X-RAY DIFFRACTIONf_angle_d0.7042901
X-RAY DIFFRACTIONf_dihedral_angle_d7.7761269
X-RAY DIFFRACTIONf_chiral_restr0.048309
X-RAY DIFFRACTIONf_plane_restr0.004369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-3.08960.35791410.26882667X-RAY DIFFRACTION100
3.0896-3.88690.30341400.23692669X-RAY DIFFRACTION100
3.8869-18.7940.251410.20482663X-RAY DIFFRACTION100
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)
13.55740.7231.12955.47250.71825.04520.41380.2626-0.05310.0853-0.35930.23990.3875-0.0379-0.00470.41880.00970.10930.3420.02230.2692-4.9923-34.7134-14.1907
24.8763-2.662-0.78573.87571.80157.9332-0.0966-0.3221.04730.12360.6053-1.1851-0.72450.93810.10580.4503-0.03780.01650.3726-0.05870.57373.2253-22.6406-1.4271
32.4581-1.4605-0.33814.81980.80263.3362-0.026-0.08290.63770.032-0.07940.3422-0.6448-0.676-0.04840.42460.1767-0.01820.4634-0.03060.5305-14.4781-12.3066-4.4716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 204 through 243 )
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 486 )

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