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- PDB-2r3h: Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r3h
TitleCrystal Structure of Cyclin-Dependent Kinase 2 with inhibitor
ComponentsCell division protein kinase 2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE / INHIBITION / CYCLIN-DEPENDENT KINASE / CANCER / ATP-binding / Cell division / Mitosis / Nucleotide-binding / Phosphorylation / Polymorphism
Function / homology
Function and homology information


Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-SCE / Uncharacterized protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFischmann, T.O. / Hruza, A.W. / Madison, V.M. / Duca, J.S.
CitationJournal: Biopolymers / Year: 2008
Title: Structure-guided discovery of cyclin-dependent kinase inhibitors.
Authors: Fischmann, T.O. / Hruza, A. / Duca, J.S. / Ramanathan, L. / Mayhood, T. / Windsor, W.T. / Le, H.V. / Guzi, T.J. / Dwyer, M.P. / Paruch, K. / Doll, R.J. / Lees, E. / Parry, D. / Seghezzi, W. / Madison, V.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2422
Polymers34,0031
Non-polymers2391
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.090, 70.680, 72.140
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 Cell division protein kinase 2 / p33 protein kinase


Mass: 34002.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: unidentified baculovirus / Strain (production host): SF9 / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-SCE / 3-methyl-N-(pyridin-4-ylmethyl)imidazo[1,2-a]pyrazin-8-amine


Mass: 239.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 50 mM Na-HEPES pH 7.4, 50 mM Ammonium Acetate, 8% v/v PEG 4000, 4% v/v Glycerol, 1 mM TCEP, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.951 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2002 / Details: PT/PD-COATED ULE MIRROR
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 43774 / % possible obs: 97.8 % / Rmerge(I) obs: 0.047 / Χ2: 1.013 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.510.346180.97955.6
1.51-1.530.3829760.99788.8
1.53-1.540.3679641.03588.7
1.54-1.550.35210491.07794.2
1.55-1.570.33310691.00996.8
1.57-1.580.32610931.04498.3
1.58-1.60.31410721.06199.9
1.6-1.620.32211271.06599.6
1.62-1.630.26910930.977100
1.63-1.650.26411050.991100
1.65-1.670.23510841.057100
1.67-1.690.2211111.033100
1.69-1.710.20911040.98999.9
1.71-1.730.20211191.059100
1.73-1.750.17910881.025100
1.75-1.780.1711231.027100
1.78-1.80.14910860.987100
1.8-1.830.14611121.034100
1.83-1.860.13211011.068100
1.86-1.890.11511191.013100
1.89-1.920.1111011.061100
1.92-1.960.09711061.057100
1.96-20.08911160.959100
2-2.040.07911160.955100
2.04-2.080.07711161.028100
2.08-2.130.07311221.024100
2.13-2.180.0710910.98100
2.18-2.240.06511280.99599.9
2.24-2.310.06111221.01399.9
2.31-2.380.05711101.006100
2.38-2.470.05611331.042100
2.47-2.560.05311250.962100
2.56-2.680.04911301.073100
2.68-2.820.04711221.04999.7
2.82-30.04311440.93299.9
3-3.230.0411210.88899.7
3.23-3.560.03511591.15399.7
3.56-4.070.03411491.06399.7
4.07-5.130.03211640.97699
5.13-500.03211860.76494.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
BUSTER-TNTrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BUSTER-TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2232 -RANDOM
Rwork0.195 ---
all0.196 44718 --
obs0.196 43450 97.2 %-
Displacement parametersBiso mean: 33.625 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 21 207 2632

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