SMTL ID : 4gne.1

Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- THR- LYS- GLN- THR: Histone H3.3(Non-covalent)

ALA-ARG-THR-LYS-GLN-THR.1: 15 residues within 4Å: Chain A: Q.12, H.14, E.15, D.16, G.24, G.25, E.26, L.27, V.28, M.29, C.30, D.31, P.50, G.52, W.54 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.16, A:W.54 Hydrogen bonds: A:Q.12, A:D.16, A:D.16, A:D.16, A:G.25, A:G.25, A:E.26, A:E.26, A:L.27, A:L.27, A:M.29, A:C.30, A:G.52 Water bridges: A:H.14, A:H.14, A:G.52 Salt bridges: A:D.31

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.18, C.21, H.40, C.43 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:H.40, A:C.43 ZN.3: 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.4: 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.5: 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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase NSD3

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