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- PDB-2pmn: Crystal structure of PfPK7 in complex with an ATP-site inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pmn
TitleCrystal structure of PfPK7 in complex with an ATP-site inhibitor
ComponentsSer/Thr protein kinase, putative
KeywordsTRANSFERASE / Ser/Thr protein kinase / Plasmodium falciparum / phosphorylation
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / mitogen-activated protein kinase kinase / MAP kinase kinase activity / protein kinase activity / phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Chem-K51 / mitogen-activated protein kinase kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMerckx, A. / Echalier, A. / Noble, M. / Endicott, J.
CitationJournal: Structure / Year: 2008
Title: Structures of P. falciparum protein kinase 7 identify an activation motif and leads for inhibitor design.
Authors: Merckx, A. / Echalier, A. / Langford, K. / Sicard, A. / Langsley, G. / Joore, J. / Doerig, C. / Noble, M. / Endicott, J.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Ser/Thr protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7562
Polymers41,4351
Non-polymers3211
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.406, 82.084, 138.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ser/Thr protein kinase, putative


Mass: 41434.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFB0605w / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7YTF7
#2: Chemical ChemComp-K51 / 4-(6-{[(1S)-1-(HYDROXYMETHYL)-2-METHYLPROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZONITRILE


Mass: 321.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH7.5; 20% PEG10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 10971 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.871 Å / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.1 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfPK7 in complex with ATP analogue (2PML)

2pml


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.872 / SU B: 39.317 / SU ML: 0.393 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29559 499 4.8 %RANDOM
Rwork0.2192 ---
obs0.22277 9946 98.22 %-
all-10971 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.814 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---0.57 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 24 55 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222942
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.983954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2524.863146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62115574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5431512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022182
X-RAY DIFFRACTIONr_nbd_refined0.2240.21440
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.24
X-RAY DIFFRACTIONr_mcbond_it0.4631.51743
X-RAY DIFFRACTIONr_mcangle_it0.83922764
X-RAY DIFFRACTIONr_scbond_it0.76231372
X-RAY DIFFRACTIONr_scangle_it1.244.51190
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 38 -
Rwork0.373 627 -
obs--86.81 %
Refinement TLS params.Method: refined / Origin x: -11.52 Å / Origin y: -24.66 Å / Origin z: -20.386 Å
111213212223313233
T0.017 Å2-0.028 Å20.0859 Å2-0.0352 Å2-0.0359 Å2---0.052 Å2
L3.057 °2-0.524 °20.5371 °2-3.852 °2-1.4059 °2--3.601 °2
S0.1929 Å °0.2802 Å °0.2164 Å °-0.3629 Å °-0.136 Å °-0.0109 Å °-0.1207 Å °-0.0232 Å °-0.0569 Å °

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