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

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Basic information

Entry
Database: PDB / ID: 4ftr
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-5HK / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 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 1.3Nov 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)32,8495
Polymers32,1541
Non-polymers6954
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.088, 65.688, 57.899
Angle α, β, γ (deg.)90.000, 94.750, 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, 126 molecules

#2: Chemical ChemComp-5HK / 2-[3-(3-methoxy-4-nitrophenyl)-11-oxo-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-8-yl]-N,N-dimethylacetamide


Mass: 446.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N4O5
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
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: 2.25→20 Å / Num. all: 16066 / Num. obs: 15809 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Χ2: 1.069 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.330.23215361.008197.6
2.33-2.420.19315851.002198.3
2.42-2.530.15615791.008198.7
2.53-2.670.1215891.035199.3
2.67-2.830.09215850.979199.2
2.83-3.050.06815861.147198.9
3.05-3.360.05215851.054199.1
3.36-3.840.04115981.206198.6
3.84-4.830.03315871.13198.4
4.83-200.03315791.118195.5

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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: 2.25→19.68 Å / Cor.coef. Fo:Fc: 0.9499 / Cor.coef. Fo:Fc free: 0.9402 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 793 5.02 %RANDOM
Rwork0.1722 ---
obs0.1742 15791 98.15 %-
Displacement parametersBiso max: 161.6 Å2 / Biso mean: 41.9517 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.5485 Å20 Å2-1.5895 Å2
2---1.9064 Å20 Å2
3---0.3579 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 48 122 2228
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1005SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes352HARMONIC5
X-RAY DIFFRACTIONt_it2206HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion272SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2582SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2206HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3018HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion2.73
LS refinement shellResolution: 2.25→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2171 142 5.06 %
Rwork0.1798 2662 -
all0.1817 2804 -
obs--98.15 %
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)
1-0.2175-0.42981.25400.92831.3141-0.00010.032-0.016-0.0342-0.01030.0030.0222-0.01390.01040.0367-0.0135-0.03290.0752-0.031-0.11677.9408-3.0395.2959
22.83850.4987-0.20172.3470.02551.4591-0.0096-0.0151-0.097-0.0776-0.0583-0.04290.0461-0.01480.068-0.10250.0186-0.007-0.11230.0037-0.049516.3306-0.549328.1689
30.09580.11060.00950.56970.05230.0009-0.00170.00880.01340.0047-0.00340.0055-0.00620.00220.0051-0.02420.02190.0341-0.0409-0.00770.072823.798814.974629.6263
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 - 271}A258 - 271

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