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- PDB-5w1y: SETD8 in complex with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 5w1y
TitleSETD8 in complex with a covalent inhibitor
ComponentsN-lysine methyltransferase KMT5A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / structural genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator ...histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of double-strand break repair via homologous recombination / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / transcription corepressor activity / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain ...Class V SAM-dependent methyltransferases / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-9SV / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTempel, W. / Yu, W. / Li, Y. / Blum, G. / Luo, M. / Pittella-Silva, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: SETD8 in complex with a covalent inhibitor
Authors: Tempel, W. / Yu, W. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionJun 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Structure summary / Category: audit_author / refine / Item: _refine.details
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _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 KMT5A
B: N-lysine methyltransferase KMT5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,27740
Polymers37,5482
Non-polymers72938
Water3,747208
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-16 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.348, 39.788, 131.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe macromolecular assembly was not a focus of this crystal structure

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Components

#1: Protein N-lysine methyltransferase KMT5A / H4-K20-HMTase KMT5A / Histone-lysine N-methyltransferase KMT5A / Lysine N-methyltransferase 5A / ...H4-K20-HMTase KMT5A / Histone-lysine N-methyltransferase KMT5A / Lysine N-methyltransferase 5A / Lysine-specific methylase 5A / PR/SET domain-containing protein 07 / PR/SET07 / SET domain-containing protein 8


Mass: 18774.191 Da / Num. of mol.: 2 / Mutation: C343S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5A, PRSET7, SET07, SET8, SETD8 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical ChemComp-9SV / 2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl)naphthalene-1,4-dione / BOUND FORM


Mass: 364.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.04 Å3/Da / Density % sol: 39.67 % / Mosaicity: 0.3 °
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M sodium fluoride, 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→43.7 Å / Num. obs: 34422 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Net I/σ(I): 15 / Num. measured all: 132133 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.733.60.657644317690.6980.3860.7661.896.3
9-43.73.40.0199182710.9990.0110.0234196.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ij8

4ij8


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.094 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.12
Details: COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Density for residue 239 (chain A) resembles a seryl side chain with alternate conformations. ...Details: COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Density for residue 239 (chain A) resembles a seryl side chain with alternate conformations. Geometry restraints for the covalent ligand were prepared with GRADE, which used MOGUL. The length of the covalent link was restrained to 1.75 A, consistent with the mean length found in a MOGUL search. Following analysis of merging statistics, only measurements on images 1..100 were included in the merging step.
RfactorNum. reflection% reflection
Rfree0.2371 1373 4 %
Rwork0.2011 --
obs0.2025 32998 99.18 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.56 Å2 / Biso mean: 20.283 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.29 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 74 208 2743
Biso mean--18.51 24.64 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192652
X-RAY DIFFRACTIONr_bond_other_d0.0020.022408
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9553590
X-RAY DIFFRACTIONr_angle_other_deg0.9873.0015598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01724.173127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7221518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023091
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
X-RAY DIFFRACTIONr_mcbond_it1.8341.8841294
X-RAY DIFFRACTIONr_mcbond_other1.8331.8841295
X-RAY DIFFRACTIONr_mcangle_it2.6342.8221620
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 98 -
Rwork0.256 2339 -
all-2437 -
obs--97.01 %

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