SMTL ID : 3tg4.1

Structure of SMYD2 in complex with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SAM.1: 16 residues within 4Å: Chain A: G.16, K.17, G.18, R.19, H.137, C.181, N.182, A.203, L.204, M.205, N.206, H.207, Y.240, Y.258, F.260 Ligands: GOL.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.17, A:R.19, A:R.19, A:N.206, A:H.207, A:H.207, A:Y.240, A:Y.258 Water bridges: A:K.17, A:K.17, A:R.19, A:E.135 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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 ZN.4: 4 residues within 4Å: Chain A: C.209, C.262, C.264, C.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.209, A:C.262, A:C.264, A:C.267

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: C.181, N.182, G.183, F.184, A.203, Y.240, Y.258 Ligands: SAM.1, GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.183 GOL.6: 7 residues within 4Å: Chain A: G.183, F.184, T.185, Y.217, Y.240, Y.258 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.185, A:T.185, A:Y.258 GOL.7: 9 residues within 4Å: Chain A: C.209, L.243, R.250, E.266, K.272, K.276, H.373, Y.374, P.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.243, A:R.250, A:E.266, A:K.272, A:K.276 GOL.8: 5 residues within 4Å: Chain A: E.190, L.351, K.387, R.390, L.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.190, A:R.390 GOL.9: 5 residues within 4Å: Chain A: A.38, Y.39, Y.41, Y.54, K.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.38, A:Y.41, A:K.115, A:K.115 Water bridges: A:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structure of human SMYD2 reveals the basis of p53 tumor suppressor methylation. J.Biol.Chem. (2011)

Release Date

2011-08-31

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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