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

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Basic information

Entry
Database: PDB / ID: 4fsm
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 / 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-HK1 / 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 1.1May 29, 2013Group: Other
Revision 1.2Nov 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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7115
Polymers32,1541
Non-polymers5574
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.050, 66.543, 57.831
Angle α, β, γ (deg.)90.000, 94.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32154.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Production host: HOMO SAPIENS (human)
References: UniProt: O14757, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-HK1 / 4-(6,7-dimethoxy-2,4-dihydroindeno[1,2-c]pyrazol-3-yl)phenol


Mass: 308.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


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


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
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→20 Å / Num. all: 15818 / Num. obs: 15818 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.062 / Χ2: 1.102 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.380.27214680.797199.1
2.38-2.480.21515000.818199.9
2.48-2.590.17115090.894199.9
2.59-2.730.12914890.9311100
2.73-2.90.10415030.911100
2.9-3.120.07615111.0151100
3.12-3.430.06215191.2331100
3.43-3.930.04815081.6281100
3.93-4.930.03715251.489199.9
4.93-200.0315561.2191100

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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→19.89 Å / Cor.coef. Fo:Fc: 0.9478 / Cor.coef. Fo:Fc free: 0.9328 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 796 5.03 %RANDOM
Rwork0.1752 ---
obs0.1764 15818 90.98 %-
Displacement parametersBiso max: 117.85 Å2 / Biso mean: 32.0693 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.2714 Å20 Å20.2842 Å2
2---1.3985 Å20 Å2
3---1.1271 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 38 191 2325
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1026SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes353HARMONIC5
X-RAY DIFFRACTIONt_it2235HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
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_contact2654SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2235HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3054HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 152 5.42 %
Rwork0.26 2655 -
all0.2617 2807 -
obs--90.98 %
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)
10.52841.45531.23020.6572.9232.9220.06440.0094-0.03830.1391-0.0582-0.0263-0.0219-0.0591-0.0063-0.0071-0.0020.05830.09260.0084-0.110811.523-4.9959-3.6326
21.5348-2.10540.40190.07970.24641.32180.07010.1016-0.14420.0698-0.0348-0.03290.1115-0.0743-0.03530.0515-0.0381-0.00840.0702-0.0161-0.129312.1169-4.69650.4632
32.94330.67061.06972.38540.50623.3007-0.01750.4114-0.0866-0.43450.0130.2280.2713-0.44930.0046-0.0153-0.0552-0.01120.0538-0.0138-0.1489.2634-1.954611.7608
44.03780.1311-0.65691.70830.15241.1914-0.06180.3196-0.047-0.21940.0260.0533-0.0243-0.05510.0358-0.06960.01480.0075-0.07250.0114-0.055914.83413.292621.5759
53.33151.48822.371801.2761.9807-0.0217-0.14710.0463-0.1379-0.03080.0858-0.0299-0.09630.0524-0.0705-0.02490.0960.0427-0.0270.1186-2.7302-0.653432.8909
62.76560.9133-0.28531.6953-0.07051.7035-0.0111-0.3309-0.20590.1352-0.087-0.11040.08430.03960.0982-0.06470.02090.0056-0.02220.03220.00319.5839-2.020136.3173
72.55751.7303-0.5642.5991-1.7468-0.1105-0.00540.15270.1143-0.0049-0.05850.00950.01930.09560.0639-0.08210.0239-0.0032-0.0545-0.0150.079928.642717.818121.6221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 17}A3 - 17
2X-RAY DIFFRACTION2{A|21 - 40}A21 - 40
3X-RAY DIFFRACTION3{A|51 - 97}A51 - 97
4X-RAY DIFFRACTION4{A|98 - 158}A98 - 158
5X-RAY DIFFRACTION5{A|159 - 166}A159 - 166
6X-RAY DIFFRACTION6{A|167 - 260}A167 - 260
7X-RAY DIFFRACTION7{A|261 - 280}A261 - 280

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