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- PDB-5fet: Crystal Structure of PVX_084705 in presence of Compound 2 -

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Basic information

Entry
Database: PDB / ID: 5fet
TitleCrystal Structure of PVX_084705 in presence of Compound 2
ComponentscGMP-dependent protein kinase, putative
KeywordsTRANSFERASE / AGC kinase / PKG / structural genomics / malaria / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / cGMP binding / endoplasmic reticulum membrane / ATP binding / metal ion binding
Similarity search - Function
cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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. / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1TR / cGMP-dependent protein kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsWernimont, A.K. / Tempel, W. / Walker, J.R. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. ...Wernimont, A.K. / Tempel, W. / Walker, J.R. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / El Bakkouri, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal Structure of PVX_084705 in presence of Compound 2
Authors: Wernimont, A.K. / Tempel, W. / Walker, J.R. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, ...Authors: Wernimont, A.K. / Tempel, W. / Walker, J.R. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / El Bakkouri, M.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJan 13, 2016ID: 5F0D
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: cGMP-dependent protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0892
Polymers96,7271
Non-polymers3621
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)190.520, 117.250, 67.420
Angle α, β, γ (deg.)90.00, 94.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cGMP-dependent protein kinase, putative


Mass: 96726.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_084705 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: A5K0N4
#2: Chemical ChemComp-1TR / 4-[7-[(dimethylamino)methyl]-2-(4-fluorophenyl)imidazo[1,2-a]pyridin-3-yl]pyrimidin-2-amine


Mass: 362.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19FN6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 5000 MME, 5% TACSIMATE, 0.1 M HEPES, 15 MM SPERMIDINE, 25% GLYCEROL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, TEMPERATURE 293.0K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.07→45 Å / Num. obs: 27515 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 81.23 Å2 / Net I/σ(I): 15.3
Reflection shellResolution: 3.07→3.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.847 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-2000data scaling
PHASERphasing
BUSTER2.10.2refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→44.18 Å / Cor.coef. Fo:Fc: 0.8796 / Cor.coef. Fo:Fc free: 0.8666 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.946 / SU Rfree Blow DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1377 5.01 %RANDOM
Rwork0.228 ---
obs0.229 27508 99.35 %-
Displacement parametersBiso mean: 79.42 Å2
Baniso -1Baniso -2Baniso -3
1--20.9449 Å20 Å212.737 Å2
2--11.7081 Å20 Å2
3---9.2368 Å2
Refinement stepCycle: LAST / Resolution: 3.07→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 27 61 6322
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822377HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2746SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1910HARMONIC5
X-RAY DIFFRACTIONt_it12419HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.91
X-RAY DIFFRACTIONt_other_torsion15.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion860SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12339SEMIHARMONIC4
LS refinement shellResolution: 3.07→3.19 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2786 139 4.9 %
Rwork0.2432 2697 -
all0.245 2836 -
obs--98.44 %
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)
11.85961.4573-1.09021.1256-0.78490.5131-0.0098-0.2322-0.05930.11320.06140.05440.0586-0.0782-0.0516-0.21240.0658-0.1567-0.03860.1568-0.1566-8.3982-26.4744.7785
20.31171.3724-0.156200.83660.30810.11430.0726-0.27190.01860.0694-0.5170.00980.0748-0.18370.15170.0659-0.1162-0.2152-0.06370.0804-34.0988-32.413711.7978
30.84020.4404-1.22385.76180.81246.126-0.02150.09720.0107-0.16380.00910.0890.085-0.17710.01240.12780.04380.0094-0.175-0.018-0.1099-48.951-17.498-12.1042
42.3057-0.38360.60042.0353-1.55282.98740.21740.19240.0543-0.0841-0.3151-0.4325-0.3670.44880.09770.047-0.0730.1503-0.22160.0168-0.0711-31.727112.962411.1486
51.8159-0.32510.10592.399-1.63733.18960.0279-0.1472-0.00070.225-0.1261-0.08150.12230.47340.09830.09510.00620.015-0.1046-0.0046-0.1746-36.0341-6.720531.9508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - 142}
2X-RAY DIFFRACTION2{A|143 - 316}
3X-RAY DIFFRACTION3{A|317 - 398}
4X-RAY DIFFRACTION4{A|399 - 621}
5X-RAY DIFFRACTION5{A|622 - 816}

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