SMTL ID : 4gng.1 (1 other biounit)

Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.18, C.21, H.40, C.43 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:H.40, A:C.43 ZN.2: 4 residues within 4Å: Chain A: C.30, C.35, C.56, H.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:C.35, A:C.56, A:H.59 ZN.3: 4 residues within 4Å: Chain A: C.72, C.75, C.99, H.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.72, A:C.75, A:C.99, A:H.102 ZN.4: 4 residues within 4Å: Chain A: C.61, C.64, C.80, H.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:C.80, A:H.83

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: W.58, H.59, F.71, E.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.59, A:E.73 GOL.6: 6 residues within 4Å: Chain A: C.21, H.40, L.42, C.43 Chain B: R.8 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.8 GOL.7: 1 residues within 4Å: Chain B: A.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, C. et al., The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition. J.Biol.Chem. (2013)

Release Date

2013-01-02

Peptides

Histone-lysine N-methyltransferase NSD3: A
Histone H3.3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase NSD3

Histone H3.3

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