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- PDB-4jds: SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine -

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Basic information

Entry
Database: PDB / ID: 4jds
TitleSETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine
ComponentsHistone-lysine N-methyltransferase SETD7
Keywordstransferase/transferase inhibitor / SETD7 / SAM / PF-5426 / Structural Genomics Consortium / SGC / Methyltransferase / SET domain / histone modification / transcription regulation / histone lysine methyltransferase / inhibitor / S-adenosyl-L-methionine / transferase-transferase inhibitor complex
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding / chromatin organization / chromosome / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-1L4 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, A. / Wu, H. / Zeng, H. / Park, H. / El Bakkouri, M. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. ...Dong, A. / Wu, H. / Zeng, H. / Park, H. / El Bakkouri, M. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine
Authors: Dong, A. / Wu, H. / Zeng, H. / El Bakkouri, M. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD7
B: Histone-lysine N-methyltransferase SETD7
C: Histone-lysine N-methyltransferase SETD7
D: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,15649
Polymers118,7364
Non-polymers3,42045
Water17,168953
1
A: Histone-lysine N-methyltransferase SETD7
hetero molecules

A: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,07834
Polymers59,3682
Non-polymers1,71032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area24120 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53911
Polymers29,6841
Non-polymers85510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53912
Polymers29,6841
Non-polymers85511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5399
Polymers29,6841
Non-polymers8558
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.048, 134.482, 137.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

21A-779-

HOH

31D-634-

HOH

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Components

#1: Protein
Histone-lysine N-methyltransferase SETD7 / Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET domain-containing protein 7 / SET7/9


Mass: 29683.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-1L4 / N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide


Mass: 456.533 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H25FN4O3S
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 37 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 953 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: Marmosaic CCD300 / Detector: CCD / Date: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 119046 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 1.206 / Net I/σ(I): 26.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7370.63558790.615199.4
1.73-1.767.10.52559200.596199.2
1.76-1.797.10.47858870.603199.6
1.79-1.837.10.40658750.646199.3
1.83-1.877.10.31958940.676199.7
1.87-1.917.20.30858950.928199.5
1.91-1.967.30.26159020.911199.6
1.96-2.027.30.18959230.78199.8
2.02-2.077.40.17459510.99199.8
2.07-2.147.50.13858920.854199.8
2.14-2.227.50.12459470.881199.8
2.22-2.317.50.13759491.324199.9
2.31-2.417.60.10759651.071199.9
2.41-2.547.60.10859411.373199.9
2.54-2.77.60.10259961.58199.9
2.7-2.917.60.08859611.7331100
2.91-3.27.50.07760321.9581100
3.2-3.667.50.06959982.1141100
3.66-4.617.40.06460752.144199.9
4.61-507.10.06461642.073198.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
MOLREPphasing
Coot0.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9S

1o9s


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2178 / WRfactor Rwork: 0.2003 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8438 / SU B: 2.244 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1118 / SU Rfree: 0.1047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1202 1 %RANDOM
Rwork0.1986 ---
obs0.1988 118841 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 24.8969 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.64 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 273 953 8778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228182
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.97911198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55151026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42224.178359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.947151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7081530
X-RAY DIFFRACTIONr_chiral_restr0.0720.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216328
X-RAY DIFFRACTIONr_mcbond_it0.5911.54989
X-RAY DIFFRACTIONr_mcangle_it1.12828078
X-RAY DIFFRACTIONr_scbond_it1.59833193
X-RAY DIFFRACTIONr_scangle_it2.6574.53093
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 93 -
Rwork0.234 8528 -
all-8621 -
obs--98.22 %

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