SMTL ID : 3pdn.1

Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 17 residues within 4Å: Chain A: R.14, G.15, N.16, Y.124, E.130, N.132, C.180, N.181, S.202, L.203, L.204, N.205, H.206, Y.239, Y.257, F.259 Ligands: GOL.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.14, A:N.16, A:Y.124, A:E.130, A:E.130, A:N.132, A:N.132, A:N.205, A:N.205, A:H.206, A:H.206, A:Y.239, A:Y.239 Water bridges: A:R.14, A:S.202, A:L.204 pi-Stacking: A:F.259, A:F.259

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: C.238, L.240, M.242, H.366 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.242 Water bridges: A:H.366 GOL.3: 8 residues within 4Å: Chain A: N.181, S.182, F.183, S.202, I.237, Y.239, Y.257 Ligands: SFG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.202, A:Y.257 Water bridges: A:S.182, A:S.182, A:Q.256, A:Q.256 GOL.4: 7 residues within 4Å: Chain A: M.190, I.214, V.215, H.366, P.367, V.368 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.214, A:H.366 GOL.5: 2 residues within 4Å: Chain A: E.142, Q.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.142, A:Q.146 GOL.6: 7 residues within 4Å: Chain A: F.151, Q.152, I.159, Q.160, D.161, L.165, L.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.152 Water bridges: A:I.159, A:A.162 GOL.7: 9 residues within 4Å: Chain A: F.126, Y.127, P.167, A.168, F.169, D.170, E.173, A.174, K.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.170, A:D.170

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.62, C.65, H.83, C.87 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:H.83, A:C.87 ZN.9: 4 residues within 4Å: Chain A: C.49, C.52, C.71, C.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.71, A:C.75 ZN.10: 4 residues within 4Å: Chain A: C.208, C.261, C.263, C.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.208, A:C.261, A:C.263, A:C.266

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sirinupong, N. et al., Structural Insights into the Autoinhibition and Posttranslational Activation of Histone Methyltransferase SmyD3. J.Mol.Biol. (2011)

Release Date

2010-11-17

Peptides

SET and MYND domain-containing protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SET and MYND domain-containing protein 3

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