SMTL ID : 7e9s.1

Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.47, D.161, H.163 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.161, A:H.163, H2O.1, H2O.1, H2O.1

1 x J06: [(3S,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34Z,39S,43S)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-6,10,14,18,22,26,30,34-octaenyl] dihydrogen phosphate(Non-covalent)

J06.2: 26 residues within 4Å: Chain A: H.81, F.82, H.162, H.163, W.215, A.217, P.223, L.226, F.230, F.231, T.273, I.274, G.286, S.287, I.290, F.331, N.341, S.344, R.347, V.348, E.360, A.416, A.420, R.426, F.427, Y.430 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.215, A:A.217, A:L.226, A:F.230, A:F.230, A:F.231, A:F.231, A:I.274, A:F.331, A:R.347, A:V.348, A:V.348, A:A.416, A:F.427, A:Y.430 Salt bridges: A:H.81, A:H.162, A:H.163, A:R.426

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: E.591, Y.675, S.676, K.681, Y.751, M.759 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.681, A:Y.751 PEG.4: 4 residues within 4Å: Chain A: L.126, W.169, S.172, T.207 No protein-ligand interaction detected (PLIP) PEG.5: 1 residues within 4Å: Chain A: L.14 No protein-ligand interaction detected (PLIP) PEG.6: 7 residues within 4Å: Chain A: Q.502, D.505, Y.697, S.699, D.700, Q.803 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.505, A:D.700 PEG.7: 2 residues within 4Å: Chain A: D.505 Ligands: PEG.6 No protein-ligand interaction detected (PLIP)

4 x 7E8: (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE(Non-covalent)

7E8.8: 3 residues within 4Å: Chain A: Y.88, I.260, F.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.88, A:I.260, A:F.264 7E8.9: 8 residues within 4Å: Chain A: W.33, F.37, T.38, F.97, E.103, V.108, F.111, I.115 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.33, A:F.37, A:F.97, A:V.108, A:F.111 Hydrogen bonds: A:T.38, A:E.103 7E8.10: 13 residues within 4Å: Chain A: E.543, T.544, Y.545, E.597, N.604, V.605, K.606, H.692, R.776, V.777, K.778, G.779, V.781 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.778, A:V.781 Hydrogen bonds: A:E.543, A:K.606, A:K.606 Salt bridges: A:K.606, A:R.776 7E8.11: 6 residues within 4Å: Chain A: V.349, Q.350, P.351, I.415, F.418, W.422 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.349, A:I.415, A:F.418, A:W.422, A:W.422 Hydrogen bonds: A:Q.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taguchi, Y. et al., The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon. Commun Biol (2021)

Release Date

2021-09-08

Peptides

Dolichyl-phosphooligosaccharide-protein glycotransferase 3: A
a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Dolichyl-phosphooligosaccharide-protein glycotransferase 3

a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide

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