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- PDB-5vd3: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (de-phosphorylated)... -

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Basic information

Entry
Database: PDB / ID: 5vd3
TitleCRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (de-phosphorylated) IN COMPLEX WITH SARACATINIB
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / TYROSINE- AND THREONINE-SPECIFIC KINASE / MEMBRANE-ASSOCIATED PROTEIN KINASE / 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 / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity ...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 / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / nucleolus / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tyrosine/threonine-protein kinase, Cdc2 inhibitor / : / 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
Similarity search - Domain/homology
Chem-H8H / DI(HYDROXYETHYL)ETHER / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2705
Polymers34,4981
Non-polymers7724
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-4 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 54.060, 114.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase / Myt1 kinase


Mass: 34498.133 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 75-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKMYT1, MYT1 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: Q99640, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-H8H / N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE / SARACATINIB


Mass: 542.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32ClN5O5 / Comment: inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM SARACATINIB

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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: Feb 17, 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: 1.8→31.108 Å / Num. obs: 27545 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.605 % / Biso Wilson estimate: 18.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.058 / Χ2: 0.976 / Net I/σ(I): 17.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.853.6320.3214.4119960.9460.37699.8
1.85-1.93.650.2695.1719690.9610.31699.9
1.9-1.953.6470.2276.0919030.9670.267100
1.95-2.013.6590.187.5818600.9790.21199.8
2.01-2.083.6430.1389.3618050.9890.16299.8
2.08-2.153.6490.11910.917430.990.13999.5
2.15-2.233.6540.09912.5716820.9920.11699.7
2.23-2.323.6140.08414.1616250.9940.099100
2.32-2.433.6230.07315.6615690.9950.08799.7
2.43-2.553.6420.06218.2514900.9960.07399.7
2.55-2.683.6120.05420.3314150.9970.06499.1
2.68-2.853.6180.04922.2813580.9970.05899.6
2.85-3.043.5960.0425.4812600.9980.04898.8
3.04-3.293.6010.03430.1111940.9980.0498.8
3.29-3.63.5490.03133.111000.9980.03798.7
3.6-4.023.4770.02936.089840.9980.03598.8
4.02-4.653.4720.02738.378840.9990.03298.4
4.65-5.693.4940.02737.987630.9990.03198.3
5.69-8.053.3990.02637.55990.9990.03197.2
8.05-31.1083.1680.02739.893460.9990.03293.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XSCALEdata scaling
SERGUIdata collection
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VCV

5vcv


Resolution: 1.8→31.108 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 1212 4.4 %
Rwork0.1664 --
obs0.1667 27544 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 53 166 2496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032385
X-RAY DIFFRACTIONf_angle_d0.873220
X-RAY DIFFRACTIONf_dihedral_angle_d16.8611422
X-RAY DIFFRACTIONf_chiral_restr0.041333
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.87190.28081330.18992905X-RAY DIFFRACTION100
1.8719-1.95710.21371320.18522864X-RAY DIFFRACTION100
1.9571-2.06030.21891330.16512890X-RAY DIFFRACTION100
2.0603-2.18930.19651330.15792892X-RAY DIFFRACTION100
2.1893-2.35830.19951350.16172935X-RAY DIFFRACTION100
2.3583-2.59550.21941340.17132911X-RAY DIFFRACTION100
2.5955-2.97090.24741350.18052933X-RAY DIFFRACTION99
2.9709-3.7420.1891360.16632941X-RAY DIFFRACTION99
3.742-31.11280.17811410.15543061X-RAY DIFFRACTION98
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)
10.95690.0616-0.10860.4582-0.19961.0867-0.0308-0.0976-0.11840.00230.01840.05430.1734-0.02180.02590.15920.0013-0.00550.2592-0.0120.1706-23.1394-1.361610.4531
21.0610.1964-0.14751.7909-0.19191.4622-0.0050.0924-0.0069-0.02520.01630.05880.0997-0.0643-0.01880.1162-0.0094-0.00410.2797-0.04510.1316-24.59763.0444-15.0573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -11 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 360 )

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