SMTL ID : 6mon.1 (1 other biounit)

Crystal structure of human SMYD2 in complex with Nle-peptide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

Ligands

1 x LEU- NLE- SER- LYS- ARG: LYS-LEU-NLE-SER-LYS-ARG-GLY(Non-covalent)

LEU-NLE-SER-LYS-ARG.1: 16 residues within 4Å: Chain A: V.175, N.176, G.179, F.180, T.181, E.183, L.187, S.192, V.211, Y.236, I.237, D.238, Y.254, Y.340, L.375, N.376 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.180, A:F.180, A:T.181, A:Y.236, A:Y.236, A:L.375 Hydrogen bonds: A:G.179, A:T.181, A:T.181, A:E.183, A:E.183, A:L.187, A:V.211, A:Y.236, A:Y.254, A:Y.340, A:N.376

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.48, C.51, C.70, C.74 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.48, A:C.51, A:C.70, A:C.74 ZN.3: 4 residues within 4Å: Chain A: C.61, C.64, H.82, C.86 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:H.82, A:C.86 ZN.4: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.263

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

SAH.5: 16 residues within 4Å: Chain A: G.12, K.13, G.14, R.15, E.131, H.133, C.177, N.178, A.199, L.200, M.201, N.202, H.203, Y.236, Y.254, F.256 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:R.15, A:N.202, A:H.203, A:H.203, A:Y.254 Salt bridges: A:R.15 pi-Stacking: A:F.256, A:F.256

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: W.352, G.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornett, E.M. et al., A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Sci Adv (2018)

Release Date

2018-12-12

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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