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- PDB-1zlt: Crystal Structure of Chk1 Complexed with a Hymenaldisine Analog -

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Basic information

Entry
Database: PDB / ID: 1zlt
TitleCrystal Structure of Chk1 Complexed with a Hymenaldisine Analog
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE / kinase
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 / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / negative regulation of mitotic nuclear division / mitotic G2/M transition checkpoint / regulation of mitotic centrosome separation / nucleus organization / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / 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 / Activation of ATR in response to replication stress / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signal transduction in response to DNA damage / replication fork / DNA damage checkpoint signaling / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / 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 / Regulation of TP53 Activity through Phosphorylation / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / chromatin remodeling / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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-HYM / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLee, C.C. / Ng, K. / Wan, Y. / Gray, N. / Spraggon, G.
CitationJournal: To be Published
Title: Crystal Structure of Chk1 Complexed with a Hymenaldisine Analog
Authors: Lee, C.C. / Ng, K. / Wan, Y. / Gray, N. / Spraggon, G.
History
DepositionMay 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 23, 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
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2823
Polymers33,8721
Non-polymers4102
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.000, 65.643, 58.112
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1


Mass: 33871.859 Da / Num. of mol.: 1 / Fragment: Chk1Kd (Residues 1-289)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: O14757, EC: 2.7.1.37
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HYM / (4Z)-4-(2-AMINO-5-OXO-3,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE)-2,3-DICHLORO-4,5,6,7-TETRAHYDROPYRROLO[2,3-C]AZEPIN-8(1H)-ONE


Mass: 314.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9Cl2N5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: PEG8000, ammonium sulfate, cacodylate, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 34070 / Num. obs: 34070 / % possible obs: 76.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.099 / Net I/σ(I): 6.9
Reflection shellResolution: 1.74→1.85 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NVQ

1nvq


Resolution: 1.74→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1724 RANDOM
Rwork0.227 --
all-44538 -
obs-34070 -
Refinement stepCycle: LAST / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 25 204 2438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.73
LS refinement shellResolution: 1.74→1.85 Å

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