SMTL ID : 5ex3.1

Crystal structure of human SMYD3 in complex with a VEGFR1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

1 x LYS- LEU- GLY- MLY- SER- LEU- GLY: VEGFR1 peptide(Non-covalent)

LYS-LEU-GLY-MLY-SER-LEU-GLY.1: 24 residues within 4Å: Chain A: S.109, V.186, C.188, N.189, S.190, F.191, T.192, C.194, M.198, E.200, V.203, S.210, I.222, F.224, C.246, Y.247, L.248, D.249, M.250, Q.264, Y.265, H.374, V.376 Ligands: SAH.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.186, A:F.191, A:V.203, A:I.222, A:Y.247 Hydrogen bonds: A:S.190, A:T.192, A:Y.247, A:D.249, A:D.249, A:Q.264, A:Q.264 Water bridges: A:S.190, A:Y.247, A:M.250

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.57, C.60, C.79, C.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.60, A:C.79, A:C.83 ZN.3: 4 residues within 4Å: Chain A: C.70, C.73, H.91, C.95 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.73, A:H.91, A:C.95 ZN.4: 4 residues within 4Å: Chain A: C.216, C.269, C.271, C.274 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.216, A:C.269, A:C.271, A:C.274

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

SAH.5: 16 residues within 4Å: Chain A: R.22, G.23, N.24, Y.132, E.138, N.140, N.189, S.210, L.211, L.212, N.213, H.214, Y.247, Y.265, F.267 Ligands: LYS-LEU-GLY-MLY-SER-LEU-GLY.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.22, A:N.24, A:N.24, A:N.24, A:Y.132, A:E.138, A:N.140, A:H.214, A:H.214, A:Y.265 Water bridges: A:S.210 pi-Stacking: A:F.267, A:F.267

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

ACY.6: 2 residues within 4Å: Chain A: Q.168, D.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.169 ACY.7: 3 residues within 4Å: Chain A: L.284, T.285, G.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.286 ACY.8: 3 residues within 4Å: Chain A: R.402, F.405, D.406 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.402, A:F.405 Hydrogen bonds: A:D.406 ACY.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.130

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3