PDBe 5vc8

X-ray diffraction
1.8Å resolution

Crystal structure of the WHSC1 PWWP1 domain

Entry authors: Qin S, Tempel W, Dong A, Bountra C, Weigelt J, Arrowsmith CH, Edwards AM, Min J, Structural Genomics Consortium (SGC)

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase NSD2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 141 amino acids
Theoretical weight: 16.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
  • Canonical: O96028 (Residues: 211-350; Coverage: 10%)
Gene names: KIAA1090, MMSET, NSD2, TRX5, WHSC1
Sequence domains: PWWP domain
dodeca-2-deoxy-nucleotide, poorly resolved by electron density Chains: W, X, Y
Molecule details ›
Chains: W, X, Y
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*TP*(DN))-3') Chain: Z
Molecule details ›
Chain: Z
Length: 3 nucleotides
Theoretical weight: 729 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 82.99Å b: 82.99Å c: 115.4Å
α: 90° β: 90° γ: 90°
R R work R free
0.201 0.2 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided