SMTL ID : 3s7b.1

Structural Basis of Substrate Methylation and Inhibition of SMYD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

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

SAM.1: 18 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: BU3.6, NH5.7 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:H.137, A:N.206, A:N.206, A:H.207, A:H.207, A:Y.240 Water bridges: A:E.135, A:E.263 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

5 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.2: 4 residues within 4Å: Chain A: P.314, L.317, V.349, Y.352 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.314, A:L.317, A:Y.352 BU3.3: 4 residues within 4Å: Chain A: W.356, R.390, L.391, G.394 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.356 BU3.4: 4 residues within 4Å: Chain A: Y.41, Y.54, C.55, T.220 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.41, A:Y.54, A:Y.54 Hydrogen bonds: A:T.220 Water bridges: A:C.55, A:T.220 BU3.5: 2 residues within 4Å: Chain A: R.67, W.83 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.83, A:W.83 Hydrogen bonds: A:R.67, A:R.67 Water bridges: A:Q.79 BU3.6: 4 residues within 4Å: Chain A: G.18, R.19, E.135 Ligands: SAM.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.19

1 x NH5: N-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[2-(5-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide(Non-covalent)

NH5.7: 21 residues within 4Å: Chain A: T.105, L.141, K.145, I.149, A.177, V.179, N.180, C.181, N.182, G.183, F.184, T.185, S.196, A.203, T.238, S.239, Y.240, S.257, Y.258, F.259 Ligands: SAM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.180, A:F.259 Hydrogen bonds: A:N.180, A:T.185, A:T.185, A:T.238, A:T.238, A:Y.258 pi-Cation interactions: A:K.145 Halogen bonds: A:K.145

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 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.10: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferguson, A.D. et al., Structural Basis of Substrate Methylation and Inhibition of SMYD2. Structure (2011)

Release Date

2011-08-10

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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