› 5upd

X-ray diffraction
1.8Å resolution

Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)

Released:
DOI: 10.2210/pdb5upd/pdb
PDB entry 5upd coloured by chain, front view.
PDB entry 5upd coloured by chain, side view.
PDB entry 5upd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tempel W, Yu W, Dong A, Cerovina T, Bountra C, Arrowsmith CH, Edwards AM, Brown PJ, Wu H, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189853 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase NSD3 Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 26.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BZ95 (Residues: 1054-1285; Coverage: 16%)
Gene names: DC28, NSD3, WHSC1L1
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand SAM 1 x SAM
Ligand UNX 17 x UNX
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 44.16Å b: 62.81Å c: 48.84Å
α: 90° β: 109.78° γ: 90°
R-values:
R R work R free
0.186 0.184 0.218
Expression system: Escherichia coli BL21(DE3)

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