Brand  (β version)

PDB ID: 5VC8

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
UNX Unknown atom or ion PoSSuM
Non-standard Residues
Code Name Show
DN Unknown 2'-deoxynucleotide
MSE Selenomethionine
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5VC8   PDBj   RCSB PDB   PDBe
Header : DNA BINDING PROTEIN
Title : Crystal structure of the WHSC1 PWWP1 domain
Release Data : 2017-06-28
Compound :
mol_id molecule chains synonym
1 Histone-lysine N-methyltransferase NSD2 A,B Multiple myeloma SET domain-containing protein,MMSET,Nuclear SET domain-containing protein 2,Protein trithorax-5,Wolf-Hirschhorn syndrome candidate 1 protein
ec: 2.1.1.43
mol_id molecule chains
2 dodeca-2-deoxy-nucleotide, poorly resolved by electron density W,X,Y
mol_id molecule chains
3 DNA (5'-D(P*CP*TP*(DN))-3') Z
other_details: Interpretation of weak electron density in terms of an unidentified fragment of the dodecadeoxynucleotide.
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:469008)
gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1
expression_system_strain: BL21(DE3)-V2R-pRARE2
expression_system_plasmid: pET28-MHL
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Qin, S., Tempel, W., Dong, A., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
Keywords : PWWP domain, Structural Genomics Consortium, DNA BINDING PROTEIN
Exp. method : X-RAY DIFFRACTION ( 1.8000 Å )
Citation :

Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.

Zhang, M.,Yang, Y.,Zhou, M.  et al.
(2021)  Biochem.Biophys.Res.Commun.  569 : 199 - 206

PubMed: 34271259
DOI: 10.1016/j.bbrc.2021.07.017

Reaction

Chain : A, B
UniProt : O96028 (NSD2_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
L-lysyl(36)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(36)-[histone H3] + S-adenosyl-L-homocysteine - PubMed:19808676, PubMed:22099308
-
L-lysyl(36)-[histone H3] + 2 S-adenosyl-L-methionine = 2 H(+) + N(6),N(6)-dimethyl-L-lysyl(36)-[histone H3] + 2 S-adenosyl-L- homocysteine 2.1.1.357 PubMed:19808676, PubMed:22099308, PubMed:27571355, PubMed:29728617
-