SMTL ID : 6eji.2 (1 other biounit)

Structure of a glycosyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.1: 31 residues within 4Å: Chain A: G.16, A.17, R.19, V.20, F.45, Y.46, H.118, S.119, Y.123, L.146, N.166, I.189, R.191, N.195, K.196, A.221, G.222, G.245, R.246, V.247, V.250, V.266, E.267, G.268, L.269, P.270, T.271, E.275 Ligands: NA.4, NA.5, CL.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.189 Hydrogen bonds: A:G.16, A:H.118, A:N.166, A:V.247, A:V.247, A:E.267, A:G.268, A:L.269, A:T.271, A:T.271, A:T.271, A:E.275 Water bridges: A:R.19, A:V.272 Salt bridges: A:R.191, A:K.196, A:K.196

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: S.14, G.222, D.223, R.246 Ligands: CL.6 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: A.122, K.125, V.266, Y.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.122, A:K.125

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

NA.4: 5 residues within 4Å: Chain A: G.15, G.16, A.17, E.18 Ligands: UD2.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:A.17, A:E.18 NA.5: 5 residues within 4Å: Chain A: G.190, R.191, K.196 Ligands: UD2.1, CL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.191 Water bridges: A:I.189, A:K.196

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

CL.6: 5 residues within 4Å: Chain A: S.14, G.15 Ligands: UD2.1, K.2, NA.5 Ligand excluded by PLIP

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
B

WlaC protein

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