SMTL ID : 5ogl.1

Structure of bacterial oligosaccharyltransferase PglB in complex with an acceptor peptide and an lipid-linked oligosaccharide analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x GLY- ASP- GLN- ASN- ALA- THR- PPN- GLY: Substrate mimicking peptide(Non-covalent)

GLY-ASP-GLN-ASN-ALA-THR-PPN-GLY.1: 23 residues within 4Å: Chain A: T.53, T.54, N.55, D.56, N.146, R.147, Y.152, E.315, T.316, I.317, M.318, E.319, N.321, R.331, L.374, W.463, W.464, D.465, G.482, H.485, R.571, I.572, V.575 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.54, A:N.321, A:V.575 Hydrogen bonds: A:T.54, A:N.146, A:Y.152, A:T.316, A:M.318, A:E.319, A:Y.433, A:W.463, A:D.465, A:G.482, A:R.571 Salt bridges: A:R.147, A:R.331

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: D.56, D.154, E.319 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.56, A:D.154, H2O.1, H2O.1, H2O.1 MN.3: 5 residues within 4Å: Chain A: E.62, R.65, Q.73, D.76, D.475 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, A:D.475, H2O.1

1 x 9UB: [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid(Non-covalent)

9UB.4: 18 residues within 4Å: Chain A: D.56, A.59, F.60, Y.79, Y.196, S.198, S.201, A.205, V.286, Q.289, Y.293, L.365, M.368, R.375, F.376, Y.379, Y.468, G.483 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.59, A:F.60, A:Y.79, A:Q.289, A:Y.293, A:L.365, A:L.365, A:F.376, A:Y.379, A:Y.468 Hydrogen bonds: A:Y.196, A:Y.196, A:S.198, A:Q.289, A:Q.289, A:R.375, A:R.375 Salt bridges: A:R.375

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

NA.5: 2 residues within 4Å: Chain A: Y.42, E.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napiorkowska, M. et al., Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-10-25

Peptides

Undecaprenyl-diphosphooligosaccharide--protein glycotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Undecaprenyl-diphosphooligosaccharide--protein glycotransferase