SMTL ID : 9ckf.1

Crystal structure of SMYD2 secondary binding site mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: S.239, Y.240, I.241, L.379, N.380 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.240, A:L.379, A:N.380 Water bridges: A:V.215, A:S.239 GOL.6: 4 residues within 4Å: Chain B: F.184, T.185, Y.240 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.185 GOL.7: 7 residues within 4Å: Chain B: C.181, G.183, F.184, A.203, Y.240, Y.258 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.181

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

SAH.2: 15 residues within 4Å: Chain A: G.16, K.17, R.19, E.135, H.137, N.182, A.203, L.204, M.205, N.206, H.207, Y.240, Y.258, F.260 Chain B: K.162 15 PLIP interactions: 1 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:K.162, A:K.17, A:R.19, A:R.19, A:E.135, A:E.135, A:E.135, A:H.207, A:H.207, A:Y.258 Water bridges: A:E.263, A:E.263 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260 SAH.8: 14 residues within 4Å: Chain B: K.17, R.19, L.129, E.135, H.137, 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 B Hydrogen bonds: B:R.19, B:H.137, B:N.206, B:H.207, B:H.207 Salt bridges: B:R.19 pi-Stacking: B:F.260, B:F.260

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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.5: 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 B: C.65, C.68, H.86, C.90 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.68, B:H.86, B:C.90 ZN.10: 4 residues within 4Å: Chain B: C.209, C.262, C.264, C.267 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.209, B:C.262, B:C.264, B:C.267 ZN.11: 4 residues within 4Å: Chain B: C.52, C.55, C.74, C.78 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.52, B:C.55, B:C.74, B:C.78

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase SMYD2