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- PDB-1gxc: FHA domain from human Chk2 kinase in complex with a synthetic pho... -

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Basic information

Entry
Database: PDB / ID: 1gxc
TitleFHA domain from human Chk2 kinase in complex with a synthetic phosphopeptide
Components
  • SERINE/THREONINE-PROTEIN KINASE CHK2
  • SYNTHETIC PHOSPHOPEPTIDE
KeywordsPHOSPHOPROTEIN-BINDING DOMAIN / CHECKPOINT KINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


positive regulation of anoikis / mitotic DNA damage checkpoint signaling / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / : / cellular response to stress / thymocyte apoptotic process / regulation of protein catabolic process ...positive regulation of anoikis / mitotic DNA damage checkpoint signaling / response to glycoside / cellular response to bisphenol A / regulation of autophagosome assembly / mitotic intra-S DNA damage checkpoint signaling / : / cellular response to stress / thymocyte apoptotic process / regulation of protein catabolic process / negative regulation of DNA damage checkpoint / replicative senescence / mitotic spindle assembly / signal transduction in response to DNA damage / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / : / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / cellular response to gamma radiation / G2/M DNA damage checkpoint / PML body / Regulation of TP53 Activity through Methylation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / cellular response to xenobiotic stimulus / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / cell division / protein serine/threonine kinase activity / protein serine kinase activity / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Chk2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLi, J. / Williams, B.L. / Haire, L.F. / Goldberg, M. / Wilker, E. / Durocher, D. / Yaffe, M.B. / Jackson, S.P. / Smerdon, S.J.
CitationJournal: Mol.Cell / Year: 2002
Title: Structural and Functional Versatility of the Fha Domain in DNA-Damage Signaling by the Tumor Suppressor Kinase Chk2
Authors: Li, J. / Williams, B.L. / Haire, L.F. / Goldberg, M. / Wilker, E. / Durocher, D. / Yaffe, M.B. / Jackson, S.P. / Smerdon, S.J.
History
DepositionApr 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Oct 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK2
B: SYNTHETIC PHOSPHOPEPTIDE
D: SERINE/THREONINE-PROTEIN KINASE CHK2
E: SYNTHETIC PHOSPHOPEPTIDE
G: SERINE/THREONINE-PROTEIN KINASE CHK2
H: SYNTHETIC PHOSPHOPEPTIDE
J: SERINE/THREONINE-PROTEIN KINASE CHK2
K: SYNTHETIC PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)75,5878
Polymers75,5878
Non-polymers00
Water1,49583
1
A: SERINE/THREONINE-PROTEIN KINASE CHK2
B: SYNTHETIC PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: SERINE/THREONINE-PROTEIN KINASE CHK2
E: SYNTHETIC PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: SERINE/THREONINE-PROTEIN KINASE CHK2
H: SYNTHETIC PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
J: SERINE/THREONINE-PROTEIN KINASE CHK2
K: SYNTHETIC PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.824, 82.884, 129.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SERINE/THREONINE-PROTEIN KINASE CHK2 / CHK2 / CDS1


Mass: 17436.217 Da / Num. of mol.: 4
Fragment: PHOSPHOTHREONINE-BINDING DOMAIN (FHA), RESIDUES 64-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O96017, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide
SYNTHETIC PHOSPHOPEPTIDE


Mass: 1460.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 mMprotein1drop
220 mMTris-HCl1droppH8.0
312 %PEG200001reservoir
40.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 24148 / % possible obs: 97.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.1
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.38 / % possible all: 87
Reflection
*PLUS
Lowest resolution: 15 Å / Redundancy: 3.5 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.514 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1214 5.1 %RANDOM
Rwork0.231 ---
obs0.232 22601 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 83 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.3761.9355770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023334
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.32023
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3321.52468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65223958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14631808
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.844.51812
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 90
Rwork0.347 1611
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)
18.95783.25584.90946.54383.18637.8426-0.22680.1754-0.0350.00070.1937-0.2818-0.57860.35090.03310.14430.0131-0.09240.18250.04650.291993.2982.396128.863
24.31672.7155-2.97565.2344-2.65496.9432-0.2354-0.3491-0.17470.14390.0369-0.27490.04110.15430.19860.08120.03420.00660.2435-0.01140.274773.76560.581110.125
37.86742.72190.093112.07593.62077.78250.1791-0.20740.62680.0927-0.71222.14730.2157-1.50780.5330.3167-0.08290.09860.5851-0.17140.892160.81782.24493.229
48.3656-1.4373-2.78745.39580.73936.59-0.43520.5587-1.1428-0.7734-0.0682-0.27520.59010.00040.50340.5767-0.25370.23410.2624-0.07490.479883.65661.58777.677
518.96574.543-2.466413.9547-0.724722.95430.2030.29990.00040.12250.30210.23770.074-1.0281-0.50510.1380.0343-0.19890.3032-0.13940.379880.41276.885117.878
622.83899.1372-6.394812.3924-7.406918.1892-0.92650.723-0.21760.08460.88110.83081.6282-0.87260.04540.322-0.08270.1180.3530.16780.351260.70349.39114.623
732.138716.512712.277715.011512.683240.25930.22270.19821.72641.3507-0.57793.10651.0789-2.90260.35520.48310.16980.41520.6634-0.45961.151463.26394.91106.112
829.2587-3.2037-15.57410.8478-3.4871-1.1596-1.0551.8980.0383-1.25140.6710.7258-0.1596-1.07790.3840.465-0.1361-0.06160.48860.1160.350771.16574.70279.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 207
2X-RAY DIFFRACTION2D92 - 207
3X-RAY DIFFRACTION3G92 - 207
4X-RAY DIFFRACTION4J92 - 207
5X-RAY DIFFRACTION5B0 - 7
6X-RAY DIFFRACTION6E0 - 7
7X-RAY DIFFRACTION7H0 - 7
8X-RAY DIFFRACTION8K0 - 7
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor obs: 0.245 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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