SMTL ID : 4oqe.1

Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Fuc3NMe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, R.103, M.117, F.118, S.120, H.123 Ligands: MMF.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.22, A:Y.33, A:A.58, A:L.80, A:S.81, A:D.101, A:M.102, A:R.103, A:S.120 Water bridges: A:G.62, A:H.64, A:M.117 Salt bridges: A:K.31, A:H.64 SAH.3: 19 residues within 4Å: Chain B: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, M.117, F.118, S.120, H.123 Ligands: MMF.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.22, B:A.58, B:L.80, B:S.81, B:D.101, B:M.102, B:S.120 Water bridges: B:G.62, B:M.117 Salt bridges: B:H.64

2 x MMF: dTDP-3-N-methylamino-3,6-dideoxygalactose(Non-covalent)

MMF.2: 19 residues within 4Å: Chain A: Y.14, K.29, F.118, H.123, W.152, W.153, N.157, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, H.210, I.212, R.241 Ligands: SAH.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.153, A:Y.162 Hydrogen bonds: A:Y.14, A:Y.14, A:N.157, A:T.159, A:S.179, A:S.181, A:R.241, A:R.241 Salt bridges: A:K.29, A:K.29, A:R.177, A:R.177, A:R.177, A:R.241 pi-Stacking: A:W.153, A:W.153 MMF.4: 19 residues within 4Å: Chain B: Y.14, K.29, F.118, H.123, W.152, W.153, N.157, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, H.210, I.212, R.241 Ligands: SAH.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.153, B:Y.162, B:Y.162 Hydrogen bonds: B:Y.14, B:Y.14, B:N.157, B:T.159, B:S.179, B:S.181, B:R.241, B:R.241 Water bridges: B:K.29, B:F.118 Salt bridges: B:K.29, B:K.29, B:R.177, B:R.177, B:R.177, B:R.241 pi-Stacking: B:W.153, B:W.153, B:Y.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Production of a novel N-monomethylated dideoxysugar. Biochemistry (2014)

Release Date

2014-02-26

Peptides

dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase

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