SMTL ID : 6n3g.1

Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

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

SAH.1: 15 residues within 4Å: Chain A: G.16, K.17, 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:R.19, A:E.135, A:H.137, A:H.207, A:H.207, A:Y.240 Water bridges: A:E.263 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

1 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.2: 13 residues within 4Å: Chain A: E.190, S.192, K.309, H.310, Y.344, G.348, L.351, Y.352, W.356, K.387, R.390, L.391, G.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.309, A:H.310, A:K.387

2 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.3: 3 residues within 4Å: Chain A: Y.258 Ligands: EOH.5, EOH.7 No protein-ligand interaction detected (PLIP) NI.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 8 residues within 4Å: Chain A: F.184, V.202, A.203, L.204, M.205, T.238, Y.240 Ligands: NI.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.184, A:T.238, A:Y.240 Hydrogen bonds: A:M.205, A:M.205 EOH.6: 4 residues within 4Å: Chain A: P.15, G.16, K.17, E.263 No protein-ligand interaction detected (PLIP) EOH.7: 5 residues within 4Å: Chain A: G.183, T.185, Y.240, Y.258 Ligands: NI.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.258 EOH.8: 1 residues within 4Å: Chain A: R.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.67 EOH.9: 3 residues within 4Å: Chain A: D.188, E.190, S.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.190, A:S.192

3 x ZN: ZINC ION(Non-covalent)

ZN.10: 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.11: 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.12: 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

Perry, E. et al., Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol. To be Published

Release Date

2019-11-20

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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