SMTL ID : 9ckc.1 (1 other biounit)

Crystal structure of SMYD2 in complex with two PARP1 peptides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-2-mer

Ligands

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

SAH.1: 17 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 Chain B: K.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:N.206, A:H.207, A:H.207, A:Y.240, A:Y.258 Water bridges: A:E.135, A:E.135, A:E.135, A:E.263, A:E.263 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.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

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
Poly [ADP-ribose] polymerase 1, processed C-terminus: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

N-lysine methyltransferase SMYD2

Poly [ADP-ribose] polymerase 1, processed C-terminus

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