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- PDB-1v0o: Structure of P. falciparum PfPK5-Indirubin-5-sulphonate ligand complex -

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Basic information

Entry
Database: PDB / ID: 1v0o
TitleStructure of P. falciparum PfPK5-Indirubin-5-sulphonate ligand complex
ComponentsCELL DIVISION CONTROL PROTEIN 2 HOMOLOG
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / CDK
Function / homology
Function and homology information


[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / RNA polymerase II CTD heptapeptide repeat kinase activity / axonogenesis / cell cycle / phosphorylation / cell division ...[RNA-polymerase]-subunit kinase / synaptic vesicle transport / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / vesicle-mediated transport / RNA polymerase II CTD heptapeptide repeat kinase activity / axonogenesis / cell cycle / phosphorylation / cell division / protein serine kinase activity / ATP binding / nucleus / metal ion binding / 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, ATP binding site / Protein kinases ATP-binding region signature. ...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, ATP binding site / Protein kinases ATP-binding region signature. / 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-INR / Cyclin-dependent kinase 2 homolog
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHolton, S. / Merckx, A. / Burgess, D. / Doerig, C. / Noble, M. / Endicott, J.
CitationJournal: Structure / Year: 2003
Title: Structures of P. Falciparum Pfpk5 Test the Cdk Regulation Paradigm and Suggest Mechanisms of Small Molecule Inhibition
Authors: Holton, S. / Merckx, A. / Burgess, D. / Doerig, C. / Noble, M. / Endicott, J.
History
DepositionMar 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
B: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7714
Polymers66,0862
Non-polymers6852
Water4,558253
1
A: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3852
Polymers33,0431
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3852
Polymers33,0431
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.562, 88.277, 63.857
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELL DIVISION CONTROL PROTEIN 2 HOMOLOG / PFPK5


Mass: 33043.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q07785, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-INR / 2',3-DIOXO-1,1',2',3-TETRAHYDRO-2,3'-BIINDOLE-5'-SULFONIC ACID / INDIRUBIN-5-SULPHONATE


Mass: 342.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPLAYS A KEY ROLE IN THE CONTROL OF THE EUKARYOTIC CELL CYCLE. IT IS REQUIRED IN HIGHER CELLS FOR ...PLAYS A KEY ROLE IN THE CONTROL OF THE EUKARYOTIC CELL CYCLE. IT IS REQUIRED IN HIGHER CELLS FOR ENTRY INTO S-PHASE AND MITOSIS.

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→25.08 Å / Num. obs: 49359 / % possible obs: 94.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.015

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.25 Å / SU B: 5.128 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.28178 2518 5.1 %RANDOM
Rwork0.23262 ---
obs-46827 97 %-
Displacement parametersBiso mean: 29.671 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20.05 Å2
2--3.93 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 48 253 4749

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