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- PDB-6cby: Crystal structure of human SET and MYND Domain Containing protein... -

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Basic information

Entry
Database: PDB / ID: 6cby
TitleCrystal structure of human SET and MYND Domain Containing protein 2 with MTF9975
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE/INHIBITOR / SMYD2 MTF9975 inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / 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 / nucleus / metal ion binding / 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 ...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 / SET domain superfamily / 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
Chem-EW4 / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsZENG, H. / DONG, A. / Hutchinson, A. / Seitova, A. / TATLOCK, J. / KUMPF, R. / OWEN, A. / TAYLOR, A. / Casimiro-Garcia, A. / Bountra, C. ...ZENG, H. / DONG, A. / Hutchinson, A. / Seitova, A. / TATLOCK, J. / KUMPF, R. / OWEN, A. / TAYLOR, A. / Casimiro-Garcia, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2019
Title: Selective, Small-Molecule Co-Factor Binding Site Inhibition of a Su(var)3-9, Enhancer of Zeste, Trithorax Domain Containing Lysine Methyltransferase.
Authors: Taylor, A.P. / Swewczyk, M. / Kennedy, S. / Trush, V.V. / Wu, H. / Zeng, H. / Dong, A. / Ferreira de Freitas, R. / Tatlock, J. / Kumpf, R.A. / Wythes, M. / Casimiro-Garcia, A. / Denny, R.A. ...Authors: Taylor, A.P. / Swewczyk, M. / Kennedy, S. / Trush, V.V. / Wu, H. / Zeng, H. / Dong, A. / Ferreira de Freitas, R. / Tatlock, J. / Kumpf, R.A. / Wythes, M. / Casimiro-Garcia, A. / Denny, R.A. / Parikh, M.D. / Li, F. / Barsyte-Lovejoy, D. / Schapira, M. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Owen, D.R.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
B: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,17410
Polymers99,7782
Non-polymers1,3968
Water93752
1
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5875
Polymers49,8891
Non-polymers6984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5875
Polymers49,8891
Non-polymers6984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.819, 117.579, 65.013
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211

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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: 49889.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EW4 / [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl)-3-methylazetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone / MTF9975


Mass: 501.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H39N7O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.21 Å3/Da / Density % sol: 44.41 % / Mosaicity: 1.042 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 28751 / % possible obs: 98.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 56.41 Å2 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.098 / Rrim(I) all: 0.227 / Χ2: 1.958 / Net I/σ(I): 4 / Num. measured all: 151491
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.595.10.93414260.4890.4531.0410.57899.2
2.59-2.645.20.82414370.6660.3970.9180.62899.2
2.64-2.695.30.78114220.6750.370.8670.66299.2
2.69-2.755.30.71214310.750.340.7920.78299.3
2.75-2.815.20.65314300.7520.3150.7280.76299.1
2.81-2.875.20.5414590.8220.260.6010.89999.5
2.87-2.944.70.49114140.8110.2470.5520.99997.7
2.94-3.025.10.43214330.8610.2090.4821.09799
3.02-3.115.60.40414460.880.1880.4471.16699.5
3.11-3.215.50.35814190.8870.1670.3961.33199
3.21-3.335.50.3114360.9180.1440.3431.59799.3
3.33-3.465.40.26914530.9330.1270.2981.89699.4
3.46-3.625.40.24114530.9420.1140.2682.44799
3.62-3.8150.2114080.940.1040.2352.94299.4
3.81-4.055.10.18614340.9620.0910.2073.40397.3
4.05-4.365.50.16914380.9650.080.1873.64899.1
4.36-4.85.30.14914400.9730.0720.1663.89199.1
4.8-5.495.30.14414570.9760.0680.163.16999.6
5.49-6.925.40.13814350.9740.0650.1542.97298.3
6.92-505.30.10614800.9840.0520.1183.98397.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementResolution: 2.55→43.59 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.874 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.734 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.258 876 3.12 %RANDOM
Rwork0.199 ---
obs0.201 28052 98.9 %-
Displacement parametersBiso mean: 52.24 Å2
Baniso -1Baniso -2Baniso -3
1-14.9079 Å20 Å2-1.1246 Å2
2---2.8051 Å20 Å2
3----12.1028 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.55→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 80 52 6540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016642HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099039HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2197SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1035HARMONIC5
X-RAY DIFFRACTIONt_it6642HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion18.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion863SEMIHARMONIC5
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_contact7663SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.282 -3.03 %
Rwork0.232 2853 -
all0.234 2942 -
obs--99.02 %
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)
11.0524-0.3683-0.02351.79870.24080.6296-0.02810.07820.1269-0.0279-0.0176-0.0954-0.0697-0.01720.0457-0.04390.0190.0712-0.147-0.0241-0.1261.9916-0.981523.7422
22.3697-0.1992-0.98141.03470.79861.9252-0.23160.4997-0.08640.04310.03440.07870.2002-0.33390.1972-0.1319-0.02730.0655-0.1921-0.0724-0.140129.3382-31.59269.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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