SMTL ID : 3rib.1 (1 other biounit)

Human lysine methyltransferase Smyd2 in complex with AdoHcy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 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.3: 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

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 17 residues within 4Å: Chain A: G.16, K.17, G.18, R.19, E.135, H.137, C.181, N.182, A.203, L.204, M.205, N.206, H.207, Y.240, Y.258, F.260 Ligands: SO4.11 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:E.135, A:N.206, A:H.207, A:H.207, A:Y.258 Water bridges: A:E.135 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: H.397, K.398, A.399, A.400 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.398, A:A.399, A:A.400 Salt bridges: A:H.397 SO4.6: 7 residues within 4Å: Chain A: C.181, N.182, G.183, F.184, Y.240, Y.258 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.181 SO4.7: 7 residues within 4Å: Chain A: T.105, L.108, V.179, G.183, F.184, T.185, S.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.196 SO4.8: 6 residues within 4Å: Chain A: G.183, F.184, T.185, Y.240, Y.258 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.185, A:Y.258 SO4.9: 4 residues within 4Å: Chain A: D.252, R.253, D.256, R.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.252, A:D.256, A:R.299 Salt bridges: A:R.253 SO4.10: 8 residues within 4Å: Chain A: C.209, L.243, E.266, K.272, K.276, H.373, Y.374, P.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.374 Salt bridges: A:K.272, A:K.276 SO4.11: 5 residues within 4Å: Chain A: P.15, G.16, K.17, E.263 Ligands: SAH.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.263, A:E.263 Salt bridges: A:K.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins. J Mol Cell Biol (2011)

Release Date

2011-07-20

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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