SMTL ID : 6yuh.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: R.12, G.13, N.14, Y.122, E.128, N.130, C.178, N.179, S.200, L.201, L.202, N.203, H.204, Y.237, Y.255, F.257 Ligands: GOL.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:Y.122, A:E.128, A:N.130, A:N.130, A:N.203, A:N.203, A:H.204, A:H.204, A:Y.237 Water bridges: A:R.12, A:R.12, A:R.12, A:E.128, A:E.128, A:S.200, A:D.260, A:D.260 pi-Stacking: A:F.257, A:F.257

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: C.178, N.179, S.180, F.181, S.200, Y.237, Y.255 Ligands: SAM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.180, A:S.200, A:Y.255 GOL.7: 4 residues within 4Å: Chain A: E.128, N.130, N.132, K.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.128, A:N.130, A:N.132, A:N.132 Water bridges: A:N.14, A:E.128 GOL.8: 6 residues within 4Å: Chain A: D.239, L.241, K.327, D.330, Y.356, V.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.295, A:K.327, A:K.327 Water bridges: A:D.239, A:D.239

1 x POW: Diperodon(Non-covalent)

POW.3: 10 residues within 4Å: Chain A: A.186, E.187, I.337, V.369, M.372, K.373, K.376, L.377, L.408, D.411 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.187, A:I.337, A:V.369, A:K.373, A:K.376, A:K.376, A:K.376, A:L.377, A:L.377, A:L.408, A:L.408 Hydrogen bonds: A:E.187, A:E.187, A:K.376 Salt bridges: A:D.411 pi-Cation interactions: A:K.373, A:K.376

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.206, C.259, C.261, C.264 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.206, A:C.259, A:C.261, A:C.264 ZN.5: 4 residues within 4Å: Chain A: C.47, C.50, C.69, C.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.47, A:C.50, A:C.69, A:C.73 ZN.6: 4 residues within 4Å: Chain A: C.60, C.63, H.81, C.85 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.60, A:C.63, A:H.81, A:C.85

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

2021-01-13

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3