SMTL ID : 6gxc.1

Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide and a reactive lipid-linked oligosaccharide analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

monomer

Ligands

1 x GLY- ASP- GLN- DAB- ALA- THR- PPN- GLY: GLY-ASP-GLN-DAB-ALA-THR-PPN-GLY

GLY-ASP-GLN-DAB-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, Y.433, W.463, W.464, D.465, G.482, I.572, V.575 Ligands: FFK.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.54, A:T.316, A:I.572, A:V.575 Hydrogen bonds: A:N.146, A:Y.152, A:T.316, A:M.318, A:E.319, A:W.463, A:D.465 Salt bridges: A:R.147, A:R.331

2 x MN: MANGANESE (II) ION

MN.2: 4 residues within 4Å: Chain A: D.56, D.154, D.156, E.319 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.56, A:D.154 MN.3: 4 residues within 4Å: Chain A: R.65, Q.73, D.76, D.475 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.76, A:D.475

1 x NA: SODIUM ION

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

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

MES.5: 6 residues within 4Å: Chain A: M.190, M.237, L.238, A.239, W.240, K.243 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.243

1 x PEG: DI(HYDROXYETHYL)ETHER

PEG.6: 2 residues within 4Å: Chain A: Y.89, W.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.90

1 x FFK: [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] [oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl] hydrogen phosphate

FFK.7: 21 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, A.364, L.365, M.368, R.375, F.376, Y.379, Y.468, G.482, G.483 Ligands: GLY-ASP-GLN-DAB-ALA-THR-PPN-GLY.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.56, A:A.59, A:F.60, A:Y.79, A:A.205, A:Q.289, A:Q.289, A:A.364, A:L.365, A:F.376, A:Y.379, A:Y.468 Hydrogen bonds: A:Y.196, A:S.198, A:Q.289 Salt bridges: A:R.375, A:R.375, A:R.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napiorkowska, M. et al., Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide. Sci Rep (2018)

Release Date

2018-11-14

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