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- PDB-4ft3: Crystal Structure of the CHK1 -

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Basic information

Entry
Database: PDB / ID: 4ft3
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 / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / 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 / 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 / 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-H1K / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)32,9238
Polymers32,1861
Non-polymers7377
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.987, 65.753, 57.920
Angle α, β, γ (deg.)90.000, 94.030, 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: 32186.049 Da / Num. of mol.: 1 / Fragment: unp residues 2-280
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

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Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-H1K / 1-(5-chloro-2,4-dimethoxyphenyl)-3-pyrazin-2-ylurea


Mass: 308.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13ClN4O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.67 %
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: 2.1→20 Å / Num. all: 19845 / Num. obs: 17166 / % possible obs: 86.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.097 / Χ2: 1.002 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.170.1926950.834135.3
2.17-2.260.1711480.875158.1
2.26-2.360.17515691.005179.1
2.36-2.490.16318280.975193.1
2.49-2.640.15719601.014198.8
2.64-2.850.14819740.983199.9
2.85-3.130.13319751.09199.9
3.13-3.590.10819911.0231100
3.59-4.510.08419921.019199.8
4.51-200.06120340.9371100

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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: 2.5→19.95 Å / Cor.coef. Fo:Fc: 0.9392 / Cor.coef. Fo:Fc free: 0.9098 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.476 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 612 5.22 %RANDOM
Rwork0.1675 ---
obs0.1699 11719 99.8 %-
Displacement parametersBiso max: 115.24 Å2 / Biso mean: 29.4545 Å2 / Biso min: 4.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.2654 Å20 Å22.1377 Å2
2---3.6383 Å20 Å2
3----0.6271 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 48 186 2382
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1081SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes362HARMONIC5
X-RAY DIFFRACTIONt_it2329HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion289SEMIHARMONIC5
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_contact2715SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2329HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3178HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion2.75
LS refinement shellResolution: 2.5→2.74 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2477 156 5.64 %
Rwork0.1599 2609 -
all0.1645 2765 -
obs--99.8 %
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)
10.0203-0.0135-0.155200.19410.31430.001-0.00070.00270.0083-0.00150.00280.0031-0.00260.00050.0098-0.00380.01760.00930.008-0.020510.3848-3.8042-5.5778
20.1703-0.4849-0.15790.04830.84360.57630.00540.0015-0.02140.0083-0.00650.0030.0013-0.00190.00110.0401-0.0325-0.01010.0155-0.0094-0.06511.7003-6.72142.9766
3-0.02110.25560.17380.00310.18110.10550.00010.0104-0.0078-0.0085-0.00250.01530.0054-0.0170.0024-0.0162-0.0151-0.02020.04170.0097-0.02514.58771.239115.2033
40.64590.3252-0.13130.5108-0.18660.9054-0.02110.05090.0126-0.08160.0197-0.02890.0471-0.03630.0014-0.0021-0.00280.0051-0.0115-0.0016-0.03816.47720.383617.5694
50.2064-0.20020.17920.0894-0.11690.19170.00140.0045-0.0051-0.0107-0.00170.0006-0.00990.00460.0003-0.0008-0.023-0.01510.01180.0072-0.007517.05374.148713.8028
60.48070.5809-0.15040.13920.0638-0.008-0.0030.0002-0.0032-0.0013-0.00650.02170.0102-0.01780.0095-0.02190.01330.0264-0.0397-0.01460.05294.173-3.196531.1272
70.03140.0006-0.06050.0213-0.1388-0.0087-0.00030.0004-0.0006-0.00040.0003-0.00110.0042-0.00190-0.00640.01430.0178-0.00210.01550.01454.9291-8.364541.5379
80.43840.42760.29290.79750.90410.0598-0.0053-0.0148-0.01120.02310.0006-0.02010.02960.02150.0047-0.00990.0482-0.0077-0.03150.05330.017520.458-4.324835.25
90.1388-0.0550.19470-0.07740.11750.00050.00130.00130.0028-0.0033-0.00630.00170.00360.0028-0.01030.0162-0.0350.03080.0457-0.006631.9123-2.340941.1232
100.1990.1616-0.75290.1525-0.09090.1357-0.0027-0.00630.01450.0337-0.009-0.0019-0.00740.00450.0117-0.03110.0277-0.01990.0253-0.00750.002920.36165.663437.3299
110.00550.0219-0.03870.11430.0806-0.00550.00040.00190.00310.0049-0.00040.0018-0.00190.00220-0.00310.0030.0284-0.0166-0.00520.024422.637814.880931.5737
12-0.02520.2540.17770.0616-0.0320.03670.00060.0050.0004-0.0006-0.00410.00480.00220.0010.00350.0089-0.0080.00870.0051-0.0028-0.006432.95719.890412.2924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 14}A2 - 14
2X-RAY DIFFRACTION2{A|15 - 42}A15 - 42
3X-RAY DIFFRACTION3{A|50 - 69}A50 - 69
4X-RAY DIFFRACTION4{A|70 - 138}A70 - 138
5X-RAY DIFFRACTION5{A|139 - 149}A139 - 149
6X-RAY DIFFRACTION6{A|150 - 179}A150 - 179
7X-RAY DIFFRACTION7{A|180 - 183}A180 - 183
8X-RAY DIFFRACTION8{A|184 - 222}A184 - 222
9X-RAY DIFFRACTION9{A|223 - 232}A223 - 232
10X-RAY DIFFRACTION10{A|233 - 259}A233 - 259
11X-RAY DIFFRACTION11{A|260 - 267}A260 - 267
12X-RAY DIFFRACTION12{A|268 - 280}A268 - 280

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