SMTL ID : 6g7d.1

Structure of MeT1 from Mycobacterium hassiacum in complex with SAM and glycerol.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 23 residues within 4Å: Chain A: G.19, F.20, M.21, E.44, G.46, T.47, Y.48, K.51, S.52, D.71, H.72, G.75, S.76, H.79, G.122, K.123, S.124, D.141, G.142, G.143, R.151 Ligands: GOL.3, CL.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.48 Hydrogen bonds: A:F.20, A:Y.48, A:S.52, A:H.72, A:G.75, A:G.75, A:S.124, A:D.141, A:G.143, A:R.151, A:R.151 Water bridges: A:T.18, A:G.50, A:K.51 pi-Stacking: A:H.72, A:H.72 SAH.7: 23 residues within 4Å: Chain B: G.19, F.20, M.21, E.44, G.46, T.47, Y.48, K.51, S.52, D.71, H.72, G.75, S.76, H.79, G.122, K.123, S.124, D.141, G.142, G.143, R.151 Ligands: GOL.9, CL.12 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.48 Hydrogen bonds: B:F.20, B:Y.48, B:S.52, B:H.72, B:G.75, B:G.75, B:S.124, B:D.141, B:G.143, B:R.151, B:R.151 Water bridges: B:T.18, B:G.50, B:K.51, B:T.100 pi-Stacking: B:H.72, B:H.72

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain B: K.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.123 Water bridges: B:K.123 GOL.3: 8 residues within 4Å: Chain A: F.20, E.78, H.79, D.141, H.144, D.170 Ligands: SAH.1, MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.79 Water bridges: A:Y.85, A:Y.85, A:D.141, A:H.169, A:H.169 GOL.8: 1 residues within 4Å: Chain A: K.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.123 Water bridges: A:K.123 GOL.9: 8 residues within 4Å: Chain B: F.20, E.78, H.79, D.141, H.144, D.170 Ligands: SAH.7, MG.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.78, B:H.79 Water bridges: B:Y.85, B:Y.85, B:D.141, B:H.169

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.141, H.169, D.170 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.141, A:H.169, A:D.170, H2O.1, H2O.1 MG.5: 1 residues within 4Å: Chain A: D.112 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.112, H2O.2, H2O.5, H2O.6, H2O.7 MG.10: 4 residues within 4Å: Chain B: D.141, H.169, D.170 Ligands: GOL.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.141, B:H.169, B:D.170, H2O.12, H2O.12 MG.11: 1 residues within 4Å: Chain B: D.112 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.112, H2O.13, H2O.16, H2O.17, H2O.18

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: K.123, S.124, A.125, R.151 Ligands: SAH.1 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: K.123, S.124, A.125, R.151 Ligands: SAH.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ripoll-Rozada, J. et al., Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2019-01-16

Peptides

Methyltransferase domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Methyltransferase domain protein

Related Entries With Identical Sequence