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- PDB-5loh: Kinase domain of human Greatwall -

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Basic information

Entry
Database: PDB / ID: 5loh
TitleKinase domain of human Greatwall
ComponentsSerine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall
KeywordsTRANSFERASE / Kinase domain / Inhibitor
Function / homology
Function and homology information


female meiosis II / MASTL Facilitates Mitotic Progression / : / cleavage furrow / regulation of mitotic cell cycle / protein phosphatase 2A binding / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / non-specific serine/threonine protein kinase ...female meiosis II / MASTL Facilitates Mitotic Progression / : / cleavage furrow / regulation of mitotic cell cycle / protein phosphatase 2A binding / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase greatwall, catalytic domain / : / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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. ...Serine/threonine-protein kinase greatwall, catalytic domain / : / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Serine/threonine-protein kinase greatwall
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRajasekaran, M.B. / Pearl, L.H. / Oliver, A.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
EU 7th FrameworkPIIF-GA-2011-301062 United Kingdom
CitationJournal: Oncotarget / Year: 2016
Title: A first generation inhibitor of human Greatwall kinase, enabled by structural and functional characterisation of a minimal kinase domain construct.
Authors: Ocasio, C.A. / Rajasekaran, M.B. / Walker, S. / Le Grand, D. / Spencer, J. / Pearl, F.M. / Ward, S.E. / Savic, V. / Pearl, L.H. / Hochegger, H. / Oliver, A.W.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall
B: Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5848
Polymers76,4292
Non-polymers1,1556
Water1,00956
1
A: Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7794
Polymers38,2151
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8054
Polymers38,2151
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.897, 80.283, 179.939
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 Serine/threonine-protein kinase greatwall,Serine/threonine-protein kinase greatwall / hGWL / Microtubule-associated serine/threonine-protein kinase-like / MAST-L


Mass: 38214.508 Da / Num. of mol.: 2 / Fragment: UNP residues 1-194,UNP residues 740-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASTL, GW, GWL, THC2 / Plasmid: pTHREE-E / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q96GX5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.03667 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03667 Å / Relative weight: 1
ReflectionResolution: 3→48.05 Å / Num. obs: 13060 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.182 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.286 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.381 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSOct 15, 2015data reduction
Aimless0.3.5data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1W

1h1w


Resolution: 3.1→48.05 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 27.4
RfactorNum. reflection% reflection
Rfree0.2653 1109 5.13 %
Rwork0.2061 --
obs0.2091 13060 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 83 56 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034033
X-RAY DIFFRACTIONf_angle_d0.6095516
X-RAY DIFFRACTIONf_dihedral_angle_d14.6622407
X-RAY DIFFRACTIONf_chiral_restr0.041609
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.24110.36441380.29882539X-RAY DIFFRACTION100
3.2411-3.41190.36951280.28172574X-RAY DIFFRACTION99
3.4119-3.62560.32061530.26842577X-RAY DIFFRACTION100
3.6256-3.90540.2831170.21412600X-RAY DIFFRACTION99
3.9054-4.29820.23611540.16892546X-RAY DIFFRACTION99
4.2982-4.91970.22761300.15912546X-RAY DIFFRACTION99
4.9197-6.19620.22261460.1922601X-RAY DIFFRACTION100
6.1962-48.05620.25791430.2022540X-RAY DIFFRACTION99

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