SMTL ID : 6ejj.1 (1 other biounit)

Structure of a glycosyltransferase / state 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x NDG- A2G- A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-A2G-A2G.1: 14 residues within 4Å: Chain A: A.10, N.13, S.14, G.15, G.16, A.17, E.18, L.95, T.97, T.98, Y.123, R.191 Ligands: UDP.2, BUE.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.13 Hydrogen bonds: A:G.16, A:A.17, A:E.18, A:E.18, A:R.191, A:T.97

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 22 residues within 4Å: Chain A: S.14, G.15, G.16, R.19, F.45, Y.46, I.189, R.191, K.196, A.221, G.222, G.245, R.246, V.247, V.250, P.270, T.271, V.272, E.275 Ligands: NDG-A2G-A2G.1, NA.4, CL.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.189 Hydrogen bonds: A:G.16, A:Y.46, A:V.247, A:V.247, A:T.271, A:T.271, A:V.272, A:E.275 Water bridges: A:K.196 Salt bridges: A:R.191, A:K.196, A:K.196

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Ligands: BUE.6 No protein-ligand interaction detected (PLIP) NA.4: 3 residues within 4Å: Chain A: E.267 Ligands: UDP.2, CL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.267, A:G.268, A:L.269

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

CL.5: 4 residues within 4Å: Chain A: A.17, H.118 Ligands: UDP.2, NA.4 Ligand excluded by PLIP

1 x BUE: NerylNeryl pyrophosphate(Non-covalent)

BUE.6: 6 residues within 4Å: Chain A: F.39, F.62, R.72, K.75 Ligands: NDG-A2G-A2G.1, NA.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.39 Water bridges: A:R.72, A:R.72 Salt bridges: A:R.72, A:K.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez, A.S. et al., Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nat Commun (2018)

Release Date

2018-02-07

Peptides

WlaC protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WlaC protein

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