SMTL ID : 5hil.1

Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylhomocysteine and sarcosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

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

SAH.1: 18 residues within 4Å: Chain A: R.64, A.88, T.89, G.90, N.94, D.109, G.110, S.111, M.114, A.134, D.135, W.136, R.137, L.153, G.154, S.156, H.159 Ligands: EDO.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.88, A:G.90, A:G.110, A:S.111, A:D.135, A:W.136, A:S.156 Water bridges: A:R.64, A:A.88, A:T.89, A:R.137 Salt bridges: A:R.64 pi-Stacking: A:W.136, A:W.136, A:W.136

1 x SAR: SARCOSINE(Non-covalent)

SAR.2: 6 residues within 4Å: Chain A: G.154, N.155, H.159, R.188, Y.227, M.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.155, A:Y.227 Salt bridges: A:R.188

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

EDO.3: 8 residues within 4Å: Chain A: E.68, I.72, I.73, F.93, N.94, R.97, L.98, L.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.94, A:R.97 EDO.4: 4 residues within 4Å: Chain A: D.56, W.61, N.121, H.125 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.121 EDO.5: 5 residues within 4Å: Chain A: R.188, N.189, I.193, H.204, D.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.188, A:R.188, A:N.189, A:N.189 EDO.6: 6 residues within 4Å: Chain A: W.61, E.62, A.65, R.97, Q.100, H.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.100 EDO.7: 6 residues within 4Å: Chain A: V.52, W.55, D.56, R.64, T.91 Ligands: SAH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.56, A:R.64, A:R.64 Water bridges: A:T.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, Y.R. et al., Structural Analysis of Glycine Sarcosine N-methyltransferase from Methanohalophilus portucalensis Reveals Mechanistic Insights into the Regulation of Methyltransferase Activity. Sci Rep (2016)

Release Date

2016-11-23

Peptides

Glycine sarcosine N-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycine sarcosine N-methyltransferase

Related Entries With Identical Sequence