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- PDB-9kna: NSD2-PWWP1 domain bound with compound 6 -

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Basic information

Entry
Database: PDB / ID: 9kna
TitleNSD2-PWWP1 domain bound with compound 6
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / PWWP
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / bone development / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / methylation / sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : ...: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
~{N}-(4-aminophenyl)-2-selanyl-benzamide / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsHuang, Y. / Li, Y. / Min, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Fragment Screening of NSD2-PWWP1 Identifies a Covalent Allosteric Site to Disrupt Both Methyllysine and DNA Binding
Authors: Huang, Y. / Li, Y. / Ren, Y. / Min, J.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,86413
Polymers30,2832
Non-polymers1,58111
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-105 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.163, 71.243, 76.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase NSD2 / Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / ...Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / Protein trithorax-5 / Wolf-Hirschhorn syndrome candidate 1 protein


Mass: 15141.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O96028, [histone H3]-lysine36 N-dimethyltransferase

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Non-polymers , 5 types, 49 molecules

#2: Chemical ChemComp-6Y3 / ~{N}-(4-aminophenyl)-2-selanyl-benzamide / amino-ebselen (open form)


Mass: 291.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N2OSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M BIS-TRIS (pH 5.5), and 20% (m/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.92→39.33 Å / Num. obs: 5978 / % possible obs: 99.83 % / Redundancy: 2 % / Rmerge(I) obs: 0.07585 / Net I/σ(I): 5.17
Reflection shellResolution: 2.92→3.02 Å / Rmerge(I) obs: 0.2164 / Num. unique obs: 1162

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→39.33 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2886 605 10.13 %
Rwork0.1807 --
obs0.1916 5973 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 91 38 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.058
X-RAY DIFFRACTIONf_dihedral_angle_d9.744281
X-RAY DIFFRACTIONf_chiral_restr0.053285
X-RAY DIFFRACTIONf_plane_restr0.008347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.210.32961500.19421306X-RAY DIFFRACTION100
3.21-3.680.29951420.19061321X-RAY DIFFRACTION100
3.68-4.630.26761540.15081320X-RAY DIFFRACTION100
4.63-50.28251590.19671421X-RAY DIFFRACTION100

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