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- PDB-7zvs: Crystal structure of the Schistosoma mansoni VKR2 kinase domain i... -

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Basic information

Entry
Database: PDB / ID: 7zvs
TitleCrystal structure of the Schistosoma mansoni VKR2 kinase domain in an active-like state (ADP-bound)
ComponentsVenus kinase receptor 2
KeywordsTRANSFERASE / kinase / active-like state
Function / homology
Function and homology information


guanylate cyclase activity / protein tyrosine kinase activity / membrane => GO:0016020 / ATP binding
Similarity search - Function
Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site ...Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
ADENOSINE-5'-DIPHOSPHATE / Venus kinase receptor 2
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsBeis, K. / Mathavan, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N019113/1 United Kingdom
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Identification of Inhibitors of the Schistosoma mansoni VKR2 Kinase Domain.
Authors: Mathavan, I. / Liu, L.J. / Robinson, S.W. / El-Sakkary, N. / Elatico, A.J.J. / Gomez, D. / Nellas, R. / Owens, R.J. / Zuercher, W. / Navratilova, I. / Caffrey, C.R. / Beis, K.
History
DepositionMay 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Venus kinase receptor 2
B: Venus kinase receptor 2
C: Venus kinase receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2725
Polymers116,4173
Non-polymers8542
Water0
1
A: Venus kinase receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2332
Polymers38,8061
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Venus kinase receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2332
Polymers38,8061
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Venus kinase receptor 2


Theoretical massNumber of molelcules
Total (without water)38,8061
Polymers38,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.258, 97.239, 72.944
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Venus kinase receptor 2


Mass: 38805.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D5JEH1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.8 M succinic acid, pH 7.0, 100mM KCl and 50mM NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.06→102.24 Å / Num. obs: 16396 / % possible obs: 87.3 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Net I/σ(I): 2.4
Reflection shellResolution: 3.06→3.29 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 821 / CC1/2: 0.42

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OJ9

2oj9


Resolution: 3.07→55.81 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 825 5.04 %
Rwork0.2173 --
obs0.2192 16385 60.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 54 0 7186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047342
X-RAY DIFFRACTIONf_angle_d0.8199956
X-RAY DIFFRACTIONf_dihedral_angle_d20.818988
X-RAY DIFFRACTIONf_chiral_restr0.0461122
X-RAY DIFFRACTIONf_plane_restr0.0051273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.260.431300.3467591X-RAY DIFFRACTION14
3.26-3.510.3902810.31081591X-RAY DIFFRACTION38
3.51-3.860.32781160.26432324X-RAY DIFFRACTION54
3.86-4.420.2481470.22273042X-RAY DIFFRACTION71
4.42-5.570.22472170.21163885X-RAY DIFFRACTION91
5.57-55.810.23542340.19264127X-RAY DIFFRACTION95
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)
13.752-1.7187-0.09566.8855-0.16950.17050.17960.24120.31460.3154-0.21421.03520.153-0.204-0.00280.80540.0445-0.17240.63050.03120.9042-58.422653.889.3693
23.43920.2089-0.56654.1613-0.83483.06960.2113-0.08730.1834-0.1654-0.11490.4593-0.1568-0.06160.06080.40190.0754-0.00260.3105-0.06240.3259-37.706155.761316.3188
33.32590.4087-1.43452.9572-0.3382.66220.3982-0.59260.19690.3587-0.2827-0.0775-0.49070.4684-0.1460.7536-0.1166-0.03590.6389-0.05020.3391-24.107462.060922.4206
41.78431.2603-0.75822.8202-1.04921.9964-0.104-0.95180.94010.9624-0.48131.28860.0132-0.15260.01510.8113-0.09260.34340.7807-0.19450.626-45.17835.882342.2728
51.54710.03710.90832.5372-0.2482.5539-0.1767-0.19480.0359-0.0099-0.01330.1644-0.08610.03520.01180.2380.00990.07280.3649-0.06510.3928-43.627.067125.0122
62.4677-0.0344-1.1661.8412-0.95061.7973-0.02690.1515-0.38760.1819-0.26490.743-0.2825-0.7390.00270.3024-0.13790.0680.52-0.12110.469-60.4418.957222.4925
72.7901-0.851-0.08822.9791-0.3052.88460.0320.2528-0.2211-0.4537-0.25340.40470.0887-0.1710.04750.4371-0.0153-0.1560.4999-0.19910.5453-52.200813.945513.4879
82.54120.78991.19112.57111.31742.6094-0.1806-0.0729-0.4156-0.29740.04590.20250.1687-0.39060.12190.4814-0.01520.07370.5875-0.14310.5629-7.1704-10.108916.0978
92.9642-0.8272-0.16451.5090.94982.9444-0.08220.0286-0.4717-0.02540.1228-0.0898-0.07270.37160.01150.4462-0.08110.00480.37210.02560.3081-16.45612.66127.3427
103.7442-0.15851.97431.9636-0.0724.0867-0.1262-0.8126-0.6260.44790.05820.7857-0.0954-0.13180.00750.4313-0.01330.18240.50450.15040.5305-32.53812.5236.9333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 943 through 1020 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1021 through 1188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1189 through 1257 )
4X-RAY DIFFRACTION4chain 'B' and (resid 946 through 1018 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1019 through 1113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1114 through 1204 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1205 through 1257 )
8X-RAY DIFFRACTION8chain 'C' and (resid 943 through 1018 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1019 through 1145 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1146 through 1257 )

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