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- PDB-5kjl: SMYD2 in complex with AZ378 -

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Basic information

Entry
Database: PDB / ID: 5kjl
TitleSMYD2 in complex with AZ378
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANFERASE / histone methyltransferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFerguson, A.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.
Authors: Cowen, S.D. / Russell, D. / Dakin, L.A. / Chen, H. / Larsen, N.A. / Godin, R. / Throner, S. / Zheng, X. / Molina, A. / Wu, J. / Cheung, T. / Howard, T. / Garcia-Arenas, R. / Keen, N. / ...Authors: Cowen, S.D. / Russell, D. / Dakin, L.A. / Chen, H. / Larsen, N.A. / Godin, R. / Throner, S. / Zheng, X. / Molina, A. / Wu, J. / Cheung, T. / Howard, T. / Garcia-Arenas, R. / Keen, N. / Pendleton, C.S. / Pietenpol, J.A. / Ferguson, A.D.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9385
Polymers49,3441
Non-polymers5954
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.098, 155.098, 52.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49343.582 Da / Num. of mol.: 1 / Mutation: G165E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.7→109.67 Å / Num. obs: 16893 / % possible obs: 97 % / Redundancy: 2.8 % / Biso Wilson estimate: 65.37 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2 / % possible all: 86.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s7b

3s7b


Resolution: 2.7→109.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.569 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.6 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.297
RfactorNum. reflection% reflectionSelection details
Rfree0.236 992 5.87 %RANDOM
Rwork0.172 ---
obs0.176 16889 96.6 %-
Displacement parametersBiso mean: 50.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.6415 Å20 Å20 Å2
2--3.6415 Å20 Å2
3----7.283 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→109.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 30 133 3612
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013557HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.234798HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1276SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes520HARMONIC5
X-RAY DIFFRACTIONt_it3557HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion22.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
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_contact4104SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.321 148 5.38 %
Rwork0.223 2602 -
all0.228 2750 -
obs--87.46 %
Refinement TLS params.Method: refined / Origin x: -49.2274 Å / Origin y: -18.6414 Å / Origin z: -25.5528 Å
111213212223313233
T-0.0906 Å20.0372 Å2-0.0082 Å2--0.0428 Å2-0.0704 Å2---0.1505 Å2
L1.2369 °2-0.287 °20.315 °2-1.3541 °2-0.0702 °2--1.0382 °2
S0.1109 Å °-0.0787 Å °-0.078 Å °0.0215 Å °-0.0902 Å °0.1907 Å °0.2239 Å °0.1074 Å °-0.0208 Å °
Refinement TLS groupSelection details: { A|* }

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