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- PDB-5xxd: Crystal structure of SmyD3 in complex with covalent inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 5xxd
TitleCrystal structure of SmyD3 in complex with covalent inhibitor 1
ComponentsSmyd3 methyltransferase
KeywordsTRANSFERASE/INHIBITOR / covalent inhibitor / methyltransferase / methyltransferase inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. ...Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Annexin V; domain 1 / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8NR / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.314 Å
AuthorsBaburajendran, N. / Anna E, J.
CitationJournal: To Be Published
Title: Crystal structure of SmyD3 in complex with covalent inhibitor 1
Authors: Baburajendran, N. / Anna E, J.
History
DepositionJul 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Smyd3 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5656
Polymers48,6021
Non-polymers9625
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19690 Å2
Unit cell
Length a, b, c (Å)61.458, 66.472, 107.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Smyd3 methyltransferase


Mass: 48602.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7B4*PLUS
#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: Chemical ChemComp-8NR / ethyl 4-(5,6,7,8-tetrahydroacridin-3-ylcarbonyl)piperazine-1-carboxylate


Mass: 367.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS AAH31010.1 FOR THIS SEQUENCE.

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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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium acetate, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→45.09 Å / Num. obs: 50203 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 11.7 / Num. measured all: 348727 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.715.70.971173720490.6010.4241.0641.479.4
9.07-45.095.60.03421053760.9990.0140.03727.996.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MEK

1mek


Resolution: 2.314→40.37 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 3592 10.1 %
Rwork0.2013 31964 -
obs0.2071 35556 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.81 Å2 / Biso mean: 22.1089 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: final / Resolution: 2.314→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 57 144 3586
Biso mean--22.57 18.74 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033523
X-RAY DIFFRACTIONf_angle_d0.8014752
X-RAY DIFFRACTIONf_chiral_restr0.04518
X-RAY DIFFRACTIONf_plane_restr0.006611
X-RAY DIFFRACTIONf_dihedral_angle_d4.3073055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3141-2.34460.27811000.244788898869
2.3446-2.37670.27881370.24671066120383
2.3767-2.41070.31631120.24471083119587
2.4107-2.44670.29261420.24011180132291
2.4467-2.48490.29921250.2361182130794
2.4849-2.52560.2941440.21561261140599
2.5256-2.56920.2541590.230412861445100
2.5692-2.61590.32661440.205112491393100
2.6159-2.66620.25351390.22413411480100
2.6662-2.72060.29811460.224212051351100
2.7206-2.77980.28931240.221513131437100
2.7798-2.84440.30941580.212312651423100
2.8444-2.91560.34051460.232612961442100
2.9156-2.99440.28581500.224812641414100
2.9944-3.08250.3041290.231313051434100
3.0825-3.1820.32971440.21712841428100
3.182-3.29570.31511520.204412291381100
3.2957-3.42760.26991340.21831302143699
3.4276-3.58360.23261500.19611252140299
3.5836-3.77250.25381430.186412701413100
3.7725-4.00880.23121490.17251255140499
4.0088-4.31810.21411410.17031260140198
4.3181-4.75250.18431280.15421273140197
4.7525-5.43960.21541330.17391216134997
5.4396-6.8510.20951290.18691246137596
6.851-53.31450.17161340.15891193132793

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