SMTL ID : 7bj1.1

Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: R.17, G.18, N.19, Y.127, E.133, N.135, C.183, N.184, S.205, L.206, L.207, N.208, H.209, Y.242, Y.260, F.262 Ligands: GOL.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.19, A:N.19, A:N.19, A:Y.127, A:E.133, A:N.135, A:N.135, A:N.208, A:N.208, A:H.209, A:H.209 Water bridges: A:R.17, A:R.17, A:R.17, A:E.133, A:E.133, A:D.265, A:D.265 pi-Stacking: A:F.262, A:F.262

1 x QKT: Diperodon (S-enantiomer)(Non-covalent)

QKT.2: 10 residues within 4Å: Chain A: A.191, E.192, I.342, N.343, V.374, M.377, K.378, K.381, L.382, L.413 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.192, A:I.342, A:V.374, A:K.378, A:K.381, A:K.381, A:K.381, A:L.382, A:L.413, A:L.413 Hydrogen bonds: A:E.192, A:E.192, A:K.381

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.211, C.264, C.266, C.269 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.211, A:C.264, A:C.266, A:C.269 ZN.4: 4 residues within 4Å: Chain A: C.52, C.55, C.74, C.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:C.74, A:C.78 ZN.5: 4 residues within 4Å: Chain A: C.65, C.68, H.86, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.68, A:H.86, A:C.90

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 1 residues within 4Å: Chain A: R.64 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.64, A:R.69, A:R.69 Salt bridges: A:R.64, A:R.69 ACT.7: 3 residues within 4Å: Chain A: P.102, Q.149, T.153 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.149

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: N.184, S.185, F.186, S.205, I.240, Y.242, Y.260 Ligands: SAM.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.205, A:Y.260 Water bridges: A:S.185, A:S.185, A:Y.242, A:Y.242, A:Q.259 GOL.9: 4 residues within 4Å: Chain A: C.241, L.243, M.245, H.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.245 Water bridges: A:C.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Talibov, V.O. et al., Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem (2021)

Release Date

2021-03-03

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3

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