SMTL ID : 5ex0.1

Crystal structure of human SMYD3 in complex with a MAP3K2 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.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.211, C.264, C.266, C.269 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.211, A:C.264, A:C.266, A:C.269

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

SAH.4: 16 residues within 4Å: Chain A: R.17, G.18, N.19, Y.127, N.135, C.183, N.184, S.205, L.206, L.207, N.208, H.209, Y.242, Y.260, F.262 Chain B: K.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.17, A:N.19, A:N.19, A:Y.127, A:N.135, A:H.209, A:H.209, A:Y.260 Water bridges: A:E.133, A:S.205 pi-Stacking: A:F.262, A:F.262

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 3 residues within 4Å: Chain A: R.362, R.372, L.398 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.362 Salt bridges: A:R.372 ACY.6: 5 residues within 4Å: Chain A: Q.155, I.162, D.164, A.165, L.168 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.162, A:L.168 Hydrogen bonds: A:Q.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, W. et al., Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase. J.Biol.Chem. (2016)

Release Date

2016-03-09

Peptides

Histone-lysine N-methyltransferase SMYD3: A
MAP3K2 peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Histone-lysine N-methyltransferase SMYD3

MAP3K2 peptide