SMTL ID : 6h40.1

High resolution structure of MeT1 from Mycobacterium hassiacum in complex with 3-methoxy-1,2-propanediol.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: I.4, R.5, D.6, T.7, D.8, R.61, Q.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.6, A:D.6, A:T.7, A:T.7 Water bridges: A:I.4 GOL.2: 8 residues within 4Å: Chain A: H.144, D.170, F.172, G.178, G.179, P.182 Ligands: GOL.3, FW5.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.179 Water bridges: A:H.144, A:G.179 GOL.3: 10 residues within 4Å: Chain A: F.20, E.78, H.79, D.141, H.144, D.170 Ligands: GOL.2, FW5.4, SAH.5, MG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.79 Water bridges: A:D.141, A:H.169 GOL.9: 1 residues within 4Å: Ligands: MG.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.112 GOL.10: 7 residues within 4Å: Chain B: I.4, R.5, D.6, T.7, D.8, R.61, Q.62 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.6, B:D.6, B:D.6, B:T.7, B:T.7 Water bridges: B:I.4 GOL.11: 8 residues within 4Å: Chain B: H.144, D.170, F.172, G.178, G.179, P.182 Ligands: GOL.12, FW5.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.179 Water bridges: B:H.144, B:D.170, B:G.179 GOL.12: 10 residues within 4Å: Chain B: F.20, E.78, H.79, D.141, H.144, D.170 Ligands: GOL.11, FW5.13, SAH.14, MG.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.78, B:H.79 Water bridges: B:D.141, B:H.169 GOL.18: 1 residues within 4Å: Ligands: MG.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.112

2 x FW5: (2~{S})-3-methoxypropane-1,2-diol(Non-covalent)

FW5.4: 11 residues within 4Å: Chain A: F.20, E.78, H.79, Y.85, D.141, H.144, D.170 Ligands: GOL.2, GOL.3, SAH.5, MG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.79 FW5.13: 11 residues within 4Å: Chain B: F.20, E.78, H.79, Y.85, D.141, H.144, D.170 Ligands: GOL.11, GOL.12, SAH.14, MG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.78, B:H.79

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

SAH.5: 30 residues within 4Å: Chain A: G.19, F.20, M.21, E.44, G.46, T.47, Y.48, K.51, S.52, V.70, D.71, H.72, H.73, H.74, G.75, S.76, H.79, T.100, G.122, K.123, S.124, A.125, F.139, D.141, G.142, G.143, R.151 Ligands: GOL.3, FW5.4, CL.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.48 Hydrogen bonds: A:F.20, A:Y.48, A:S.52, A:S.52, A:D.71, A:D.71, A:H.72, A:H.72, A:G.75, A:S.124, A:D.141, A:G.143, A:R.151, A:R.151 Water bridges: A:G.50, A:K.51, A:T.100 pi-Stacking: A:H.72, A:H.72 SAH.14: 30 residues within 4Å: Chain B: G.19, F.20, M.21, E.44, G.46, T.47, Y.48, K.51, S.52, V.70, D.71, H.72, H.73, H.74, G.75, S.76, H.79, T.100, G.122, K.123, S.124, A.125, F.139, D.141, G.142, G.143, R.151 Ligands: GOL.12, FW5.13, CL.17 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.48 Hydrogen bonds: B:F.20, B:Y.48, B:S.52, B:S.52, B:D.71, B:D.71, B:H.72, B:H.72, B:G.75, B:S.124, B:D.141, B:G.143, B:R.151, B:R.151 Water bridges: B:G.50, B:K.51, B:T.100 pi-Stacking: B:H.72, B:H.72

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: D.141, H.169, D.170 Ligands: GOL.3, FW5.4 6 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.141, A:H.169, A:D.170, H2O.1, H2O.1, FW5.4 MG.7: 2 residues within 4Å: Chain A: D.112 Ligands: GOL.9 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.112, H2O.1, H2O.1, H2O.1, H2O.4 MG.15: 5 residues within 4Å: Chain B: D.141, H.169, D.170 Ligands: GOL.12, FW5.13 6 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.141, B:H.169, B:D.170, H2O.12, H2O.12, FW5.13 MG.16: 2 residues within 4Å: Chain B: D.112 Ligands: GOL.18 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.112, H2O.11, H2O.12, H2O.12, H2O.15

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

CL.8: 5 residues within 4Å: Chain A: K.123, S.124, A.125, R.151 Ligands: SAH.5 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: K.123, S.124, A.125, R.151 Ligands: SAH.14 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

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