[English] 日本語
Yorodumi
- PDB-5kjn: SMYD2 in complex with AZ506 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kjn
TitleSMYD2 in complex with AZ506
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 H3K4 trimethyltransferase activity / histone H3K36 methyltransferase 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 H3K4 trimethyltransferase activity / histone H3K36 methyltransferase 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 / cytoplasm / cytosol
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
Chem-6TL / (R,R)-2,3-BUTANEDIOL / S-ADENOSYLMETHIONINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,06214
Polymers49,3441
Non-polymers1,71813
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.871, 154.871, 52.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

-
Protein , 1 types, 1 molecules A

#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
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

-
Non-polymers , 6 types, 82 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-6TL / 5-[2-[4-[2-(1~{H}-indol-3-yl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-3-carboxamide / AZ506


Mass: 536.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N6O
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.72→54.76 Å / Num. obs: 16689 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 70.55 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.72→2.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.6 / % possible all: 92.4

-
Processing

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

3s7b


Resolution: 2.72→54.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.57 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.552 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.286
RfactorNum. reflection% reflectionSelection details
Rfree0.225 845 5.06 %RANDOM
Rwork0.162 ---
obs0.165 16688 98.4 %-
Displacement parametersBiso mean: 57.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.7273 Å20 Å20 Å2
2--0.7273 Å20 Å2
3----1.4547 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.72→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 108 69 3630
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013636HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194900HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1306SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3636HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion21.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion457SEMIHARMONIC5
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_contact4097SEMIHARMONIC4
LS refinement shellResolution: 2.72→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.281 137 4.86 %
Rwork0.219 2682 -
all0.222 2819 -
obs--92.89 %
Refinement TLS params.Method: refined / Origin x: -48.8895 Å / Origin y: -18.5164 Å / Origin z: -25.412 Å
111213212223313233
T-0.0819 Å20.0361 Å2-0.0146 Å2--0.0602 Å2-0.065 Å2---0.1256 Å2
L1.4774 °2-0.3805 °20.1353 °2-1.875 °20.188 °2--1.0405 °2
S0.0535 Å °-0.058 Å °-0.0106 Å °0.0184 Å °-0.1223 Å °0.1794 Å °0.1292 Å °0.0808 Å °0.0688 Å °
Refinement TLS groupSelection details: { A|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more