SMTL ID : 9ckg.1

Crystal structure of SMYD2 active site mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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, 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:H.207, A:H.207, A:Y.258 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.65, R.67, 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 ZN.4: 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

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: K.309, H.310, Y.352 No protein-ligand interaction detected (PLIP) PEG.6: 6 residues within 4Å: Chain A: S.192, Y.344, G.348, L.351, K.387 Ligands: PG4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.192, A:K.387

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 4 residues within 4Å: Chain A: L.351, W.356, G.394 Ligands: PEG.6 No protein-ligand interaction detected (PLIP)

1 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 3 residues within 4Å: Chain A: T.185, E.187, Y.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.185

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: R.67, K.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.80, A:K.80, A:W.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding. Biorxiv (2024)

Release Date

2025-01-15

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2