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- PDB-4fsw: Crystal Structure of the CHK1 -

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Basic information

Entry
Database: PDB / ID: 4fsw
TitleCrystal Structure of the CHK1
ComponentsSerine/threonine-protein kinase Chk1
KeywordsTRANSFERASE/TRANSFERASE inhibitor / 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 / regulation of double-strand break repair via homologous recombination / nucleus organization ...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 / regulation of double-strand break repair via homologous recombination / nucleus organization / negative regulation of gene expression, epigenetic / 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 / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / peptidyl-threonine phosphorylation / Signaling by SCF-KIT / G2/M DNA damage checkpoint / 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 / chromatin remodeling / protein phosphorylation / protein domain specific binding / intracellular membrane-bounded organelle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / 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-HK6 / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKang, Y.N. / Stuckey, J.A. / Chang, P. / Russell, A.J.
CitationJournal: To be Published
Title: Crystal Structure of the CHK1
Authors: Kang, Y.N. / Stuckey, J.A. / Chang, P. / Russell, A.J.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5714
Polymers32,1701
Non-polymers4013
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.227, 65.845, 58.079
Angle α, β, γ (deg.)90.000, 94.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase Chk1 / CHK1 checkpoint homolog / Cell cycle checkpoint kinase / Checkpoint kinase-1


Mass: 32170.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: CHEK1, CHK1 / Production host: HOMO SAPIENS (human)
References: UniProt: O14757, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-HK6 / 8-chloro-5,10-dihydro-11H-dibenzo[b,e][1,4]diazepin-11-one


Mass: 244.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClN2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, Isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: Osmic Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15252 / Num. obs: 15222 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.082 / Χ2: 1.063 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.380.25715041.078199.3
2.38-2.480.23615071.1361100
2.48-2.590.17915151.1361100
2.59-2.730.14215261.1581100
2.73-2.90.12715021.1121100
2.9-3.120.115211.1291100
3.12-3.440.08615231.0871100
3.44-3.930.0715251.0621100
3.93-4.950.05615421.004199.9
4.95-500.05315570.73198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.29 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9249 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 763 5.02 %RANDOM
Rwork0.1836 ---
obs0.1851 15200 99.87 %-
Displacement parametersBiso max: 156.55 Å2 / Biso mean: 36.1617 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.1838 Å20 Å20.3076 Å2
2---0.6106 Å20 Å2
3----0.5733 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 26 176 2309
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1006SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes339HARMONIC5
X-RAY DIFFRACTIONt_it2209HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2609SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2209HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3011HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion2.76
LS refinement shellResolution: 2.3→2.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2464 130 4.78 %
Rwork0.1783 2589 -
all0.1816 2719 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.1423-0.15640.833200.76441.06540.0051-0.002-0.0075-0.0254-0.0217-0.01510.0124-0.01540.01660.0236-0.0102-0.00460.0547-0.0125-0.08638.1577-2.65794.8788
21.92320.34930.03471.80740.21781.0941-0.0158-0.0129-0.066-0.0496-0.0306-0.02940.0459-0.00160.0464-0.07120.01850.0073-0.0860.006-0.042816.5543-0.622528.182
30.05940.1719-0.14610.8673-0.2361-0.0241-0.00290.02180.0109-0.0021-0.00390.0219-0.00950.01050.0067-0.02190.01260.0273-0.0266-0.00940.046527.067517.05723.1722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 75}A3 - 75
2X-RAY DIFFRACTION2{A|76 - 257}A76 - 257
3X-RAY DIFFRACTION3{A|258 - 280}A258 - 280

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