SMTL ID : 3g5t.1

Crystal structure of trans-aconitate 3-methyltransferase from yeast

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: W.252, K.253, N.258, K.259, K.261, E.262, D.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.253 Water bridges: A:D.263 EDO.2: 9 residues within 4Å: Chain A: A.151, D.152, P.153, P.169, Y.170, R.184, Y.242, W.246 Ligands: T8N.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.152, A:D.152, A:Y.170, A:Y.170, A:R.184, A:R.184, A:Y.242 EDO.3: 9 residues within 4Å: Chain A: S.17, R.18, P.19, K.232, V.234, E.238, F.239, Y.242, W.289 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.232 EDO.4: 6 residues within 4Å: Chain A: N.10, R.13, Y.249, H.250, K.253, Q.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:Q.254 Water bridges: A:N.10 EDO.5: 5 residues within 4Å: Chain A: R.186, L.191, K.192, D.193, S.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.193, A:D.193, A:S.194 Water bridges: A:R.186, A:N.189 EDO.6: 6 residues within 4Å: Chain A: D.24, F.25, M.28, K.226, P.227, L.228 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: D.34, D.142, H.202, K.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.202 Water bridges: A:D.34, A:K.141, A:K.141 EDO.8: 4 residues within 4Å: Chain A: D.162, I.166, E.212, R.215 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.162

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

SAH.9: 23 residues within 4Å: Chain A: S.1, F.4, Y.14, Y.21, G.44, C.45, G.46, T.49, A.50, D.68, L.69, S.70, M.73, S.96, S.97, S.98, V.120, E.121, C.122, W.125, F.126, Y.150 Ligands: T8N.10 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.14, A:Y.14, A:Y.21, A:G.44, A:G.46, A:L.69, A:S.70, A:S.98, A:S.98, A:V.120 Water bridges: A:A.50, A:V.120, A:Y.150

1 x T8N: (2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid(Non-covalent)

T8N.10: 16 residues within 4Å: Chain A: F.4, Y.14, R.18, E.121, H.124, W.125, Y.150, A.151, W.179, R.184, L.187, Y.242, W.246, S.247 Ligands: EDO.2, SAH.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.187 Hydrogen bonds: A:E.121, A:W.125, A:Y.242, A:W.246, A:S.247 Water bridges: A:R.184, A:R.184 Salt bridges: A:R.18, A:R.18, A:R.18, A:H.124, A:R.184

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 2 residues within 4Å: Chain A: R.188, N.189 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgie, E.S. et al., Crystal structure of trans-aconitate 3-methyltransferase from yeast. To be Published

Release Date

2009-03-03

Peptides

Trans-aconitate 3-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Trans-aconitate 3-methyltransferase