SMTL ID : 3ooi.1

Crystal Structure of Human Histone-Lysine N-methyltransferase NSD1 SET domain in Complex with S-adenosyl-L-methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.173, C.220, C.222, C.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.173, A:C.220, A:C.222, A:C.227 ZN.2: 5 residues within 4Å: Chain A: C.45, C.47, C.55, C.61 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.45, A:C.47, A:C.55, A:C.61 ZN.3: 5 residues within 4Å: Chain A: C.55, C.70, C.75, C.81 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.55, A:C.70, A:C.75, A:C.81

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: T.99, L.100, Q.101, R.102, K.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.100, A:Q.101, A:R.102 Water bridges: A:R.11 Salt bridges: A:R.102 SO4.5: 4 residues within 4Å: Chain A: I.23, K.24, V.25, R.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.24, A:V.25, A:V.25 Salt bridges: A:R.27

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.6: 19 residues within 4Å: Chain A: R.102, G.103, W.104, T.144, N.145, F.146, Y.147, R.167, F.168, M.169, N.170, H.171, Y.208, N.215, V.219, C.220, K.221, C.222, L.231 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:W.104, A:T.144, A:N.145, A:F.146, A:F.146, A:Y.147, A:N.170, A:H.171, A:H.171, A:N.215, A:K.221 Water bridges: A:R.102, A:N.145, A:N.145, A:N.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, Q. et al., The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation. J.Biol.Chem. (2010)

Release Date

2010-12-22

Peptides

Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific