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

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Basic information

Entry
Database: PDB / ID: 4ftm
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-1HK / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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)32,8617
Polymers32,1541
Non-polymers7076
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.022, 65.957, 58.139
Angle α, β, γ (deg.)90.000, 94.670, 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) / 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, 177 molecules

#2: Chemical ChemComp-1HK / 4-[2-(2,4-dihydroindeno[1,2-c]pyrazol-3-yl)ethyl]-2-methoxyphenol


Mass: 306.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N2O2
#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.: 2 / 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.: 171 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
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: 1.9→50 Å / Num. all: 26878 / Num. obs: 26744 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056 / Χ2: 1.116 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.970.34226681.017199.8
1.97-2.050.23326761.092199.9
2.05-2.140.17526771.064199.7
2.14-2.250.13926641.043199.9
2.25-2.390.10226561.239199.8
2.39-2.580.08726881.195199.9
2.58-2.840.06526811.2191100
2.84-3.250.04826811.136199.9
3.25-4.090.03826941.08199.6
4.09-500.03526591.068196.4

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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: 1.9→44.87 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.9454 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1341 5.02 %RANDOM
Rwork0.1719 ---
obs0.1734 26706 99.49 %-
Displacement parametersBiso max: 131.7 Å2 / Biso mean: 34.1321 Å2 / Biso min: 11.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.7935 Å20 Å2-0.7915 Å2
2---1.836 Å20 Å2
3----1.9576 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 48 171 2297
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1044SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes367HARMONIC5
X-RAY DIFFRACTIONt_it2257HARMONIC20
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_contact2651SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2257HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3092HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2464 153 5.1 %
Rwork0.1972 2847 -
all0.1996 3000 -
obs--99.49 %
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)
10.0366-0.4415-0.25610.06160.7970.78530.00320.0011-0.01020.0397-0.0025-0.00110.0195-0.0139-0.00070.0486-0.00690.0170.03880.0393-0.08511.1068-4.4882-4.3505
20.26340.0707-0.28140.00130.69750.81920.01950.0342-0.03440.0249-0.0096-0.01520.0126-0.0229-0.00990.1156-0.0451-0.00610.0853-0.0339-0.197411.836-4.04840.0068
30.39260.72241.28630.41231.14360.20750.00480.10660.038-0.0656-0.04580.03460.0552-0.11450.041-0.0424-0.0463-0.07990.0960.0361-0.08494.0650.898513.6172
40.01760.01320.07360.02240.03790.10190.0006-0.0001-0.0031-0.0007-0.00090.0005-0.0008-0.00240.00040.0243-0.0336-0.02750.0138-0.02430.0031-0.1903-12.00213.5922
5-0.19110.09881.15831.01140.85640.7026-0.01130.0943-0.0574-0.17610.0192-0.11270.0626-0.0598-0.00790.0068-0.00770.05660.0471-0.0381-0.103718.1559-2.556711.4779
63.39910.0089-0.57022.5090.20141.3757-0.03230.1605-0.0323-0.26120.0394-0.0617-0.04190.0108-0.007-0.01620.01450.0006-0.04460.0111-0.026817.97913.572823.5216
70.4886-1.0436-0.24410.44590.20650.56090.0230.1515-0.034-0.1443-0.09360.0843-0.03610.02170.07070.0256-0.0335-0.00960.0298-0.0009-0.066914.85621.96815.4845
80.77370.02440.400900.11660.10720.00360.005-0.00320.0111-0.00840.0016-0.01250.00020.0048-0.13480.0272-0.0172-0.0462-0.0320.1898-4.90425.089929.9544
91.88910.65250.80620.3431-0.0590.2197-0.0038-0.0517-0.01510.0441-0.03930.08760.1259-0.13940.0431-0.0246-0.01020.0252-0.02860.00830.04927.4321-6.498232.9856
100.03530.1183-0.14570.0464-0.39170.2093-0.0005-0.0044-0.00260.01050.0010.00340.0054-0.002-0.0006-0.0178-0.04130.03050.00770.07330.03294.4294-8.33841.7088
111.44061.1461-0.29851.6042-0.27531.08390.009-0.0838-0.15070.0333-0.0435-0.11250.1114-0.05120.0344-0.03380.0144-0.0119-0.06610.01530.024518.5602-2.864432.5897
120.0548-0.60070.97870.1818-0.7830.63330.0079-0.0516-0.04770.0347-0.0281-0.00870.04860.02790.0201-0.03250.0363-0.0650.05380.10210.007325.1816-6.702143.4782
131.94761.424-0.88422.1442-1.34294.19550.0311-0.2510.0380.2799-0.0968-0.1325-0.09920.20120.0657-0.0616-0.0148-0.021-0.0344-0.0114-0.019522.6533.94337.6604
140.05760.0351-0.35690.5165-0.52230.10090.0065-0.01220.02340.0196-0.01210.0138-0.0129-0.00380.0056-0.024-0.0130.0051-0.0947-0.01060.139821.911514.486233.1549
150.15750.5879-0.35740.2835-0.15090.09710.00330.0788-0.0232-0.0523-0.01130.0518-0.01390.01170.008-0.02630.00220.0207-0.06570.01660.114930.598718.6517.2384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 16}A3 - 16
2X-RAY DIFFRACTION2{A|22 - 40}A22 - 40
3X-RAY DIFFRACTION3{A|51 - 73}A51 - 73
4X-RAY DIFFRACTION4{A|74 - 80}A74 - 80
5X-RAY DIFFRACTION5{A|81 - 97}A81 - 97
6X-RAY DIFFRACTION6{A|98 - 136}A98 - 136
7X-RAY DIFFRACTION7{A|137 - 153}A137 - 153
8X-RAY DIFFRACTION8{A|154 - 160}A154 - 160
9X-RAY DIFFRACTION9{A|161 - 179}A161 - 179
10X-RAY DIFFRACTION10{A|180 - 183}A180 - 183
11X-RAY DIFFRACTION11{A|184 - 212}A184 - 212
12X-RAY DIFFRACTION12{A|213 - 226}A213 - 226
13X-RAY DIFFRACTION13{A|227 - 259}A227 - 259
14X-RAY DIFFRACTION14{A|260 - 264}A260 - 264
15X-RAY DIFFRACTION15{A|265 - 280}A265 - 280

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