SMTL ID : 5hq8.1 (1 other biounit)

Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.212, C.265, C.267, C.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.212, A:C.265, A:C.267, A:C.270 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, H.87, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.87, A:C.91 ZN.3: 4 residues within 4Å: Chain A: C.53, C.56, C.75, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.56, A:C.75, A:C.79

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: P.171, F.173 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.171, A:F.173, H2O.11, H2O.13

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: L.348, H.386, Q.387 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: C.242, L.244, M.246, H.370 Chain B: G.12, G.13, Y.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.13 EDO.8: 3 residues within 4Å: Chain A: E.196 Chain B: G.12, G.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:D.245, A:Q.256, B:G.12 Hydrogen bonds: B:G.12

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

SAH.7: 16 residues within 4Å: Chain A: R.18, G.19, N.20, Y.128, E.134, N.136, N.185, S.206, L.207, L.208, N.209, H.210, Y.243, Y.261, F.263 Chain B: K.11 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.20, A:N.20, A:N.20, A:E.134, A:N.136, A:N.136, A:N.209, A:H.210, A:H.210 Water bridges: A:R.18, A:Y.128, A:Y.128, A:K.139, A:S.206, A:D.266 pi-Stacking: A:F.263, A:F.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Aller, G.S. et al., Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets. Structure (2016)

Release Date

2016-03-30

Peptides

Histone-lysine N-methyltransferase SMYD3: A
MEKK2 peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

Histone-lysine N-methyltransferase SMYD3

MEKK2 peptide

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