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- PDB-4e47: SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(... -

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Basic information

Entry
Database: PDB / ID: 4.0E+47
TitleSET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine
ComponentsHistone-lysine N-methyltransferase SETD7
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ternary complex / SET domain / methyltransferase / inhibitor / S-adenosylmethionine / chromatin regulator / chromosomal protein / nucleus / transcription / transcription regulation / transferase / Structural Genomics Consortium / SGC / 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 / chromosome / chromatin organization / 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-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 ...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-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 superfamily / SET domain / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-0N6 / BETA-MERCAPTOETHANOL / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWalker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. ...Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Setd7 in Complex with Inhibitor and SAM
Authors: Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / ...Authors: Walker, J.R. / Ouyang, H. / Dong, A. / Fish, P. / Cook, A. / Barsyte, D. / Vedadi, M. / Tatlock, J. / Owen, D. / Bunnage, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)122,25814
Polymers118,7364
Non-polymers3,52210
Water15,439857
1
A: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6955
Polymers29,6841
Non-polymers1,0114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5213
Polymers29,6841
Non-polymers8372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5213
Polymers29,6841
Non-polymers8372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-lysine N-methyltransferase SETD7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5213
Polymers29,6841
Non-polymers8372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.343, 133.799, 136.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 29683.951 Da / Num. of mol.: 4 / Fragment: SET domain (UNP residues 109-366)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: PHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 867 molecules

#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-0N6 / (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide


Mass: 438.543 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H26N4O3S
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 72406 / Num. obs: 72406 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 28.51 Å2 / Rsym value: 0.097 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3345 / Rsym value: 0.627 / % possible all: 92.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
BUSTER2.8.0refinement
Coot0.6model building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M53
Resolution: 2→39.88 Å / Cor.coef. Fo:Fc: 0.9572 / Cor.coef. Fo:Fc free: 0.9428 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 3632 5.02 %RANDOM
Rwork0.1595 ---
obs0.1616 72353 --
Displacement parametersBiso mean: 30.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.5841 Å20 Å20 Å2
2--0.9248 Å20 Å2
3----1.5089 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 2→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7693 0 241 857 8791
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018312HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0211362HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2728SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1224HARMONIC5
X-RAY DIFFRACTIONt_it8176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion15.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1033SEMIHARMONIC5
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_contact10087SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2308 254 5.15 %
Rwork0.1898 4678 -
all0.192 4932 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.87710.38550.21640.69070.04990.9317-0.02070.067-0.019-0.04050.0205-0.0601-0.02080.05740.0003-0.0423-0.02580.0192-0.06240.0006-0.041-26.372929.169518.7746
20.69440.3572-0.00170.86390.11021.15240.0155-0.0458-0.0739-0.00430.0065-0.04350.0698-0.0228-0.022-0.0517-0.02220.0055-0.06560.0182-0.051-54.7182-2.43917.7293
30.7073-0.18240.24410.7774-0.321.4371-0.05-0.0541-0.0355-0.00850.0780.0694-0.0016-0.0979-0.028-0.0756-0.00650.0141-0.0428-0.0023-0.0538-30.346729.944954.0801
40.8284-0.43290.4161.2908-0.86671.6225-0.0047-0.1714-0.0396-0.02510.06790.16960.0425-0.1046-0.0632-0.1276-0.0046-0.0017-0.03270.0072-0.0351-5.7396-3.132649.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A116 - 802
2X-RAY DIFFRACTION2{ B|* }B116 - 801
3X-RAY DIFFRACTION3{ C|* }C117 - 801
4X-RAY DIFFRACTION4{ D|* }D116 - 801

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