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- PDB-5vd2: crystal structure of human WEE1 kinase domain in complex with PF-... -

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Basic information

Entry
Database: PDB / ID: 5vd2
Titlecrystal structure of human WEE1 kinase domain in complex with PF-03814735
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE1 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of G2/MI transition of meiotic cell cycle / 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 ...negative regulation of G2/MI transition of meiotic cell cycle / 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 / phosphorylation / 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 / 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-34W / PHOSPHATE ION / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0815
Polymers32,4411
Non-polymers6404
Water88349
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)50.520, 45.710, 59.440
Angle α, β, γ (deg.)90.000, 102.520, 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-34W / N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide


Mass: 474.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25F3N6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 9.0 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 PF-03814735

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→34.109 Å / Num. obs: 16639 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.142 % / Biso Wilson estimate: 34.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.042 / Χ2: 0.975 / Net I/σ(I): 20.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.13.1310.2624.6512210.950.31699.7
2.1-2.163.1520.2315.4112060.9560.27999.3
2.16-2.223.120.1726.8911520.9760.20899.3
2.22-2.293.1480.167.4311460.9750.19499.6
2.29-2.373.1610.129.4710890.9860.14699.5
2.37-2.453.1460.111.3810590.990.12199.3
2.45-2.543.1380.08212.9710370.9940.199.4
2.54-2.653.1570.0715.439800.9950.08599.4
2.65-2.763.1530.05617.969430.9960.06899.1
2.76-2.93.1590.04621.868990.9970.05699.3
2.9-3.063.1630.03925.458630.9980.04798.4
3.06-3.243.1430.03430.278160.9970.04198.3
3.24-3.473.1440.02933.977630.9980.03598.3
3.47-3.743.1390.02538.57180.9980.03198.6
3.74-4.13.1430.02441.286490.9990.02998.2
4.1-4.583.1440.02343.596040.9990.02897.3
4.58-5.293.1660.02244.525110.9990.02697.1
5.29-6.483.1420.02143.444450.9990.02597.4
6.48-9.173.0950.022453490.9980.02796.4
9.17-34.1092.8250.02545.271890.9950.03289.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
SERGUIdata collection
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V5Y

5v5y


Resolution: 2.05→34.109 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.77
RfactorNum. reflection% reflection
Rfree0.2555 832 5 %
Rwork0.2034 --
obs0.206 16634 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 233.67 Å2 / Biso mean: 53.7988 Å2 / Biso min: 19.27 Å2
Refinement stepCycle: final / Resolution: 2.05→34.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 66 49 2171
Biso mean--51.01 36.78 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032142
X-RAY DIFFRACTIONf_angle_d0.5622896
X-RAY DIFFRACTIONf_chiral_restr0.045312
X-RAY DIFFRACTIONf_plane_restr0.003371
X-RAY DIFFRACTIONf_dihedral_angle_d17.5081292
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 (%)
2.05-2.17840.28261380.242426292767100
2.1784-2.34660.29721380.25162625276399
2.3466-2.58270.28341390.23582630276999
2.5827-2.95620.26551390.22852647278699
2.9562-3.72380.3121380.20882615275398
3.7238-34.11340.20451400.16912656279697
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)
10.6171-0.11370.22830.5810.4590.6860.0145-0.0073-0.4291-0.2472-0.0708-0.2079-0.2203-0.3601-0.00390.3838-0.0113-0.00720.38720.04040.483-11.0991-2.63557.2361
21.5618-0.56351.34641.3532-0.97881.9130.2667-0.2296-0.572-0.15740.25820.09040.47110.28340.86120.32350.0192-0.07430.3099-0.07980.4234-6.6773-7.15739.3157
34.28750.78611.04061.7097-0.05331.46270.2060.0013-0.27280.0286-0.145-0.12880.28690.10580.04070.2340.06390.02190.29190.02240.2736-0.38171.544113.5911
41.7053-0.20751.14020.7067-0.14610.81060.2224-1.08220.2520.1278-0.07920.4509-0.1261-0.18080.16870.35-0.09510.07940.5672-0.09030.32047.384910.754825.16
53.66150.45990.32973.4528-0.13311.88960.1850.0124-0.0339-0.1835-0.2481-0.3071-0.09870.1972-0.00010.23640.03060.01110.25910.03020.220314.02316.288513.9692
61.9203-1.50710.60252.922-0.62141.31280.2535-1.04240.96750.1147-0.2084-0.1705-0.168-0.1933-0.11940.3978-0.1411-0.00640.6236-0.17140.508218.178317.745622.1776
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 399 )A338 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 419 )A400 - 419
5X-RAY DIFFRACTION5chain 'A' and (resid 420 through 527 )A420 - 527
6X-RAY DIFFRACTION6chain 'A' and (resid 528 through 569 )A528 - 569

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