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- PDB-4gh2: Crystal Structure of the CHK1 -

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Basic information

Entry
Database: PDB / ID: 4gh2
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 / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination ...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 / inner cell mass cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / nucleus organization / 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 / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / 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 / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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-HK0 / ISOPROPYL ALCOHOL / Serine/threonine-protein kinase Chk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1137
Polymers32,1861
Non-polymers9276
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.145, 65.811, 57.993
Angle α, β, γ (deg.)90.00, 94.92, 90.00
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
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, 219 molecules

#2: Chemical ChemComp-HK0 / 3-(3-methoxy-4-nitrophenyl)-6-[2-(morpholin-4-yl)ethoxy]-5,10-dihydro-11H-dibenzo[b,e][1,4]diazepin-11-one


Mass: 490.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N4O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
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: 2.02→50 Å / Num. all: 22506 / Num. obs: 21719 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.02-2.090.19166.9
2.09-2.180.1771100
2.18-2.270.1471100
2.27-2.390.1181100
2.39-2.540.1031100
2.54-2.740.0791100
2.74-3.020.0621100
3.02-3.450.0481100
3.45-4.350.039199.9
4.35-500.038197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000data scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OT3

3ot3


Resolution: 2.03→44.98 Å / Cor.coef. Fo:Fc: 0.9522 / Cor.coef. Fo:Fc free: 0.9437 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 1116 5.14 %RANDOM
Rwork0.1638 ---
obs0.1653 21704 98.68 %-
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.2706 Å20 Å2-0.6172 Å2
2---1.8163 Å20 Å2
3---2.0869 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 62 213 2404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012305HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963164HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1049SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes364HARMONIC5
X-RAY DIFFRACTIONt_it2305HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
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_contact2827SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.13 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2426 143 5.35 %
Rwork0.2003 2532 -
all0.2025 2675 -
obs--98.68 %
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)
11.3854-0.68870.64390.46121.72214.92070.0250.1683-0.02170.4021-0.00260.060.25-0.0983-0.02240.0711-0.00640.04760.0073-0.0123-0.133411.8772-6.0056-1.3368
22.0474-2.208-1.27910-0.28291.63150.02930.06270.01570.0256-0.0281-0.06620.0539-0.0543-0.00120.1287-0.0426-0.01640.0307-0.043-0.144611.5902-3.16741.9595
32.88211.1409-0.21883.87080.62832.9612-0.00940.4745-0.0309-0.2121-0.08360.27930.1098-0.43880.093-0.0692-0.0195-0.07850.0869-0.0096-0.05993.7377-0.171912.1431
41.0070.0441.14622.19581.00784.423-0.0330.3283-0.2953-0.42130.0425-0.05130.2695-0.2582-0.00950.0111-0.040.02730.0098-0.0526-0.131715.7001-4.220310.5443
52.28880.4156-0.56471.81890.22981.5719-0.06090.19240.0191-0.18140.0389-0.0499-0.04810.02170.022-0.03680.0227-0.009-0.05260.0103-0.010817.71973.603723.2853
63.4686-0.9851-2.00781.95110.51582.6218-0.05150.23210.0222-0.4617-0.06580.1709-0.0713-0.00970.11730.0074-0.0015-0.02180.03560.0018-0.040312.02052.224817.6585
74.0703-0.51841.569801.13081.7558-0.0029-0.18680.17360.0036-0.13920.14530.0776-0.15090.142-0.12530.00440.01910.0079-0.03770.0739-3.3730.0531.6315
81.85130.2468-0.3841.98080.14561.191-0.0569-0.0992-0.24920.1007-0.00330.0160.1434-0.11430.0602-0.06550.0034-0.009-0.07450.0178-0.019515.2872-5.140133.3714
90.5404-2.12012.60370.4804-2.87824.06320.0507-0.227-0.10840.0751-0.0419-0.11540.24040.0355-0.00880.0390.0506-0.08020.10950.07360.09125.0824-6.630943.3228
103.50071.145-0.93571.5095-0.45722.50440.0127-0.51930.08070.2101-0.0765-0.1835-0.05430.20380.0637-0.07480.0084-0.0227-0.0223-0.0113-0.031322.56973.84237.4619
110.450.8965-1.52184.7904-1.41670.3390.040.08760.18050.0474-0.09250.0662-0.03740.05210.0526-0.0383-0.0079-0.0048-0.0650.01030.102324.181815.071829.9162
121.45120.0121.04550-0.47180.16930.0032-0.0266-0.0279-0.02760.0077-0.01410.0757-0.0083-0.0109-0.0231-0.0679-0.00210.10760.0710.010434.496421.39028.2231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 31}A3 - 31
2X-RAY DIFFRACTION2{A|32 - 39}A32 - 39
3X-RAY DIFFRACTION3{A|40 - 76}A40 - 76
4X-RAY DIFFRACTION4{A|77 - 97}A77 - 97
5X-RAY DIFFRACTION5{A|98 - 136}A98 - 136
6X-RAY DIFFRACTION6{A|137 - 156}A137 - 156
7X-RAY DIFFRACTION7{A|157 - 166}A157 - 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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