[English] 日本語
Yorodumi
- PDB-5v5y: CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH MK1775 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v5y
TitleCRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH MK1775
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE family / 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-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / 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 / : / 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 / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)U01 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 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2226
Polymers32,4411
Non-polymers7815
Water1,982110
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)50.080, 63.100, 82.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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-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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.75 %
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, 0.1 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 12.5 % PEG 3350, 1 mM MK1775

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2015
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: 1.9→34.515 Å / Num. obs: 21197 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.642 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 0.989 / Net I/σ(I): 22.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.955.7110.3614.8315440.9450.397100
1.95-25.6970.2726.0515160.9640.399.9
2-2.065.730.2317.1114630.9750.25499.9
2.06-2.125.7140.198.6514210.9810.20999.9
2.12-2.195.7210.15210.8613670.9880.16799.9
2.19-2.275.7020.1213.1913450.9910.13199.9
2.27-2.365.7390.10614.5513010.9930.116100
2.36-2.455.6990.09216.6912310.9950.101100
2.45-2.565.7140.07918.9411960.9960.08799.8
2.56-2.695.7080.06722.0511560.9970.07499.7
2.69-2.835.7050.05625.2210870.9980.062100
2.83-35.6530.04829.5210440.9980.05399.8
3-3.215.6270.0434.559740.9980.04499.6
3.21-3.475.5870.03540.859110.9990.03899.7
3.47-3.85.5560.02946.688420.9990.03299.5
3.8-4.255.3980.02749.417810.9990.02999.9
4.25-4.915.4210.02453.266770.9990.02799.9
4.91-6.015.4120.02650.165970.9990.02899.8
6.01-8.55.2250.02651.724720.9990.02999.2
8.5-34.5154.7350.02452.562720.9990.02796.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X8B

1x8b


Resolution: 1.9→34.515 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.2147 1059 5 %
Rwork0.1713 --
obs0.1728 21192 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.31 Å2 / Biso mean: 36.8598 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.9→34.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 109 110 2282
Biso mean--40.81 33.63 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062160
X-RAY DIFFRACTIONf_angle_d0.9772913
X-RAY DIFFRACTIONf_chiral_restr0.036311
X-RAY DIFFRACTIONf_plane_restr0.004371
X-RAY DIFFRACTIONf_dihedral_angle_d17.366806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.98640.22521310.206624912622100
1.9864-2.09120.23141300.183624752605100
2.0912-2.22210.22461300.1724632593100
2.2221-2.39370.21641310.171324902621100
2.3937-2.63450.21331320.169525082640100
2.6345-3.01550.22691320.180225172649100
3.0155-3.79850.20511330.164425302663100
3.7985-34.52090.20851400.16482659279999
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)
12.8916-0.764-2.67653.49511.00954.72690.1384-0.0759-0.1052-0.125-0.1284-0.1278-0.50360.4559-0.02650.2466-0.08290.00280.2420.00310.19126.67698.10852.2431
21.95040.58451.10481.11650.41843.27130.0187-0.15160.03830.00790.03940.0041-0.0088-0.1097-0.07220.19690.01580.00070.16050.01610.200713.8403-2.7514-2.7993
31.6867-0.5398-0.10671.29621.16962.81910.0806-0.1009-0.0834-0.0392-0.13920.3140.2237-0.99090.00390.1992-0.0941-0.00320.35430.01560.2032-0.9707-7.326-12.2534
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 484 )A338 - 484
3X-RAY DIFFRACTION3chain 'A' and (resid 485 through 569 )A485 - 569

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more