SMTL ID : 6kqq.2 (1 other biounit)

NSD1 SET domain in complex with BT3 and SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

SAM.1: 19 residues within 4Å: Chain A: R.90, G.91, W.92, T.132, N.133, F.134, Y.135, R.155, F.156, M.157, N.158, H.159, Y.196, V.207, C.208, K.209, C.210, L.219 Ligands: DQL.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:W.92, A:T.132, A:F.134, A:F.134, A:Y.135, A:Y.135, A:N.158, A:N.158, A:H.159, A:H.159, A:Y.196, A:K.209 Water bridges: A:R.90, A:N.133, A:N.133, A:N.133

1 x DQL: 2-azanyl-6-sulfanyl-1,3-benzothiazol-4-ol(Non-covalent)

DQL.2: 13 residues within 4Å: Chain A: T.132, F.134, Y.196, C.200, L.201, G.202, N.203, G.204, K.205, T.206, L.219, G.220 Ligands: SAM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.132 Water bridges: A:F.134, A:F.134 pi-Stacking: A:F.134

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.28, I.30, P.31, R.32 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.28, A:R.32 Water bridges: A:S.28, A:I.30, A:R.32, A:R.32

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.43, C.58, C.63, C.69 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.43, A:C.58, A:C.63, A:C.69 ZN.5: 5 residues within 4Å: Chain A: C.33, C.35, C.43, C.49 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.33, A:C.35, A:C.43, A:C.49 ZN.6: 4 residues within 4Å: Chain A: C.161, C.208, C.210, C.215 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.161, A:C.208, A:C.210, A:C.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Covalent inhibition of NSD1 histone methyltransferase. Nat.Chem.Biol. (2020)

Release Date

2020-09-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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