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

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Basic information

Entry
Database: PDB / ID: 4ftc
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-H6K / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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

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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)32,7846
Polymers32,1701
Non-polymers6145
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.324, 65.896, 58.120
Angle α, β, γ (deg.)90.000, 94.540, 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: 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

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-H6K / 1-(5-cyanopyrazin-2-yl)-3-(5-phenyl-1H-pyrazol-3-yl)urea


Mass: 305.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N7O
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 54.27 %
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→50 Å / Num. all: 23039 / Num. obs: 22648 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.036 / Χ2: 1.436 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.070.20821032.414192.3
2.07-2.150.1622872.26198.7
2.15-2.250.12422621.681199.8
2.25-2.370.09422891.456199.9
2.37-2.520.07623061.284199.7
2.52-2.710.05522631.257199.5
2.71-2.990.04122801.193199.3
2.99-3.420.02922881.1199
3.42-4.310.02322691.195198.4
4.31-500.02323011.199196.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.45 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9443 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1163 5.14 %RANDOM
Rwork0.169 ---
obs0.1703 22633 97.81 %-
Displacement parametersBiso max: 136.77 Å2 / Biso mean: 34.2009 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.4093 Å20 Å2-0.0046 Å2
2---3.2437 Å20 Å2
3---1.8344 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 2→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 42 184 2332
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1032SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes361HARMONIC5
X-RAY DIFFRACTIONt_it2252HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
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_contact2649SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2252HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3074HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion2.73
LS refinement shellResolution: 2→2.1 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2008 144 5.3 %
Rwork0.1862 2574 -
all0.187 2718 -
obs--97.81 %
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)
10.022-0.1-0.14430.01240.1510.21590.0008-0.00010.00110.0071-0.00130.0040.0032-0.00180.00060.00930.00050.01550.01080.0024-0.022310.469-4.0165-4.6899
20.00540.1191-0.04670.12490.44980.31790.00320.0098-0.0137-0.00050.0001-0.00170.0009-0.0004-0.00330.0318-0.01580.00810.0305-0.0321-0.074712.0476-4.44310.3989
30.02780.12470.29030.01960.04450.0459-0.0027-0.0014-0.002-0.0017-0.00290.00430.008600.0056-0.0068-0.0303-0.04350.0214-0.025-0.01250.75-6.174614.7812
4-0.03880.07490.41030.1038-0.37980.1912-0.00250.0114-0.00170.0002-0.00160.00270.0049-0.00920.00410.00930.0223-0.04510.03560.028-0.05286.25823.487111.3907
50.0026-0.2004-0.03290.23580.93990.41870.00210.0167-0.0216-0.03650.00470.00580.0071-0.0078-0.00680.0178-0.01780.04670.028-0.038-0.055715.5958-4.57110.5214
61.09040.0332-0.34651.45050.26071.3057-0.00910.08750.0116-0.12-0.0314-0.0007-0.0408-0.02720.0405-0.02680.01530.0013-0.0590.00860.008915.48843.161421.5416
70.37190.2151-0.15670.0014-0.1879-0.0262-0.001-0.00490.0097-0.0019-0.00430.0059-0.0029-0.00980.0053-0.04760.00010.01890.0002-0.040.0448-3.18630.702332.7468
80.77390.66020.16381.2049-0.01010.6582-0.0078-0.0365-0.02590.0281-0.0167-0.00670.0347-0.04410.0245-0.0190.01160.0039-0.06130.01350.059615.8877-4.93233.3665
9-0.0385-0.01410.52880.0094-0.42520.160.0002-0.0074-0.0040.0061-0.0035-0.00240.0110.00260.00330.00090.0581-0.07930.01070.0993-0.017925.4465-6.729543.3818
100.55310.8459-0.06490.7676-0.27041.24320.0067-0.05770.01390.0829-0.0354-0.034-0.01880.01930.0287-0.05470.00530.0057-0.0075-0.00470.030722.87653.861437.6601
110.0402-0.0297-0.25130.4563-0.0824-0.04020.0020.0030.00450.0011-0.00610.0026-0.0028-0.00040.00410.0013-0.00680.0145-0.08180.00710.081124.097115.42830.3211
120.04330.00060.004300.00510.01420-0.00010.0014-0.0013-0.00070.00060.00050.00030.00080.0022-0.00130.00350.00280.0007034.887621.44628.1783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 16}A2 - 16
2X-RAY DIFFRACTION2{A|21 - 40}A21 - 40
3X-RAY DIFFRACTION3{A|41 - 60}A41 - 60
4X-RAY DIFFRACTION4{A|61 - 75}A61 - 75
5X-RAY DIFFRACTION5{A|76 - 97}A76 - 97
6X-RAY DIFFRACTION6{A|98 - 157}A98 - 157
7X-RAY DIFFRACTION7{A|158 - 166}A158 - 166
8X-RAY DIFFRACTION8{A|167 - 212}A167 - 212
9X-RAY DIFFRACTION9{A|213 - 226}A213 - 226
10X-RAY DIFFRACTION10{A|227 - 259}A227 - 259
11X-RAY DIFFRACTION11{A|260 - 270}A260 - 270
12X-RAY DIFFRACTION12{A|271 - 280}A271 - 280

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