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- PDB-5th7: Complex of SETD8 with MS453 -

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Basic information

Entry
Database: PDB / ID: 5th7
TitleComplex of SETD8 with MS453
ComponentsN-lysine methyltransferase KMT5A
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
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 / negative regulation of double-strand break repair via homologous recombination / histone methyltransferase activity / 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-7BY / N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYu, W. / Tempel, W. / Babault, N. / Ma, A. / Butler, K.V. / Jin, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2016
Title: Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase.
Authors: Butler, K.V. / Ma, A. / Yu, W. / Li, F. / Tempel, W. / Babault, N. / Pittella-Silva, F. / Shao, J. / Wang, J. / Luo, M. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Jin, J.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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.ptnr2_label_seq_id

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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)34,39926
Polymers33,5622
Non-polymers83724
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-9 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.150, 31.640, 114.890
Angle α, β, γ (deg.)90.000, 105.230, 90.000
Int Tables number5
Space group name H-MC121

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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: 16780.869 Da / Num. of mol.: 2 / Fragment: UNP residues 234-380 / Mutation: C302S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5A, PRSET7, SET07, SET8, SETD8 / Plasmid: pET28MHL / 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-7BY / N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide


Mass: 387.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N5O3
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 20% PEG-3350, 0.2 M ammonium fluoride, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794535 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794535 Å / Relative weight: 1
ReflectionResolution: 1.95→37.51 Å / Num. obs: 21342 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.099 / Net I/σ(I): 11.2 / Num. measured all: 73611 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.95-22.60.8421.3357313970.6230.6111.04694.5
8.94-37.513.10.02533.57732530.9970.0180.03198.8

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished crystallographic model of human SETD8

Resolution: 1.95→37.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.154
Details: Geometry restraints for the covalent inhibitor were prepared with prodrg and grade.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1066 5 %thin shells (sftools)
Rwork0.189 ---
obs0.192 21340 99 %-
Displacement parametersBiso max: 131.89 Å2 / Biso mean: 38.29 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.7909 Å2
2--0.6537 Å20 Å2
3----0.9937 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 1.95→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 81 96 2319
Biso mean--26.24 34.88 -
Num. residues----288
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d802SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes383HARMONIC5
X-RAY DIFFRACTIONt_it2293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion306SEMIHARMONIC5
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_contact2656SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2293HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3105HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion15.56
LS refinement shellResolution: 1.95→2.04 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.245 114 4.24 %
Rwork0.22 2574 -
all-2688 -
obs--95.32 %
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)
11.47290.03910.61031.29820.62022.6899-0.059-0.1172-0.07530.13610.0507-0.0565-0.05380.1970.0083-0.04720.00230.0136-0.0750.0112-0.0636-18.5484-3.016150.6877
25.08582.04170.74412.63050.33281.4251-0.26640.74950.0494-0.2770.26980.25190.0209-0.0796-0.0034-0.1196-0.0376-0.0114-0.04580.0057-0.1539-38.0425-2.7789128.7814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|236 - A|378 }A236 - 378
2X-RAY DIFFRACTION2{ B|236 - B|378 }B236 - 378

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