SMTL ID : 6kqq.1 (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:N.158, A:H.159, A:H.159, A:H.159, A:K.209 Water bridges: A:R.90, A:N.133, A:N.133, A:N.133, A:N.133, A:R.155

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 DW9: 2-azanyl-6-[(2-azanyl-4-oxidanyl-1,3-benzothiazol-6-yl)disulfanyl]-1,3-benzothiazol-4-ol(Non-covalent)

DW9.3: 15 residues within 4Å: Chain A: D.2, K.3, K.4, P.5, K.9, H.10, I.84, G.148, P.149, K.150, G.151, N.152, Y.153, R.155, F.156 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.5, A:I.84, A:Y.153, A:Y.153, A:F.156 Hydrogen bonds: A:N.1, A:D.2, A:K.4, A:K.9, A:P.149, A:Y.153 Water bridges: A:K.4, A:K.4, A:R.155, A:R.155 pi-Cation interactions: A:R.155

3 x ZN: ZINC ION(Non-covalent)

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

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 1 residues within 4Å: Chain A: E.48 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.48, H2O.4 CA.8: 2 residues within 4Å: Chain A: E.116, K.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, A:K.141, H2O.4, H2O.8

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
A

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

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