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- PDB-3nlb: Novel kinase profile highlights the temporal basis of context dep... -

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Basic information

Entry
Database: PDB / ID: 3nlb
TitleNovel kinase profile highlights the temporal basis of context dependent checkpoint pathways to cell death
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase Domain / Checkpoint Kinase / ATP Binding / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / replication fork / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Checkpoint kinase 1, catalytic 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, ATP binding site ...Checkpoint kinase 1, catalytic 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, 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-5BE / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMassey, A.J. / Borgognoni, J. / Bentley, C. / Foloppe, N. / Fiumana, A. / Walmsley, L.
CitationJournal: Plos One / Year: 2010
Title: Context-dependent cell cycle checkpoint abrogation by a novel kinase inhibitor
Authors: Massey, A.J. / Borgognoni, J. / Bentley, C. / Foloppe, N. / Fiumana, A. / Walmsley, L.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5292
Polymers34,1481
Non-polymers3801
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.885, 65.710, 54.420
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1


Mass: 34148.148 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PFASTBAC1/CHK1 1-289 C8H / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5BE / 3-methyl-5-[5-(1-methylethyl)-1H-benzimidazol-2-yl]-N-(1-methylpiperidin-4-yl)-1H-pyrazole-4-carboxamide


Mass: 380.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 24614 / % possible obs: 87.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06 / Num. measured all: 184416

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.091 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 1107 5.2 %RANDOM
Rwork0.1807 ---
obs0.18382 20377 87.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.575 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-0.27 Å2
2--0.27 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 28 154 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222186
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9812962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36824.608102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34715388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3911512
X-RAY DIFFRACTIONr_chiral_restr0.210.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211650
X-RAY DIFFRACTIONr_mcbond_it1.4121.51301
X-RAY DIFFRACTIONr_mcangle_it2.4622103
X-RAY DIFFRACTIONr_scbond_it3.553885
X-RAY DIFFRACTIONr_scangle_it5.1354.5859
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 38 -
Rwork0.222 749 -
obs--43.34 %

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