SMTL ID : 8pn9.1

Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: R.75, R.513, N.537 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2: 15 residues within 4Å: Chain A: L.80, N.548, T.550, H.551, R.554, T.608 Chain F: I.526, Q.527, H.528, L.529 Chain H: I.360, D.361, P.362, F.363 Ligands: NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.361

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 13 residues within 4Å: Chain A: R.40, F.41, E.42, I.501 Chain E: V.291, N.299, V.300, S.301, S.303, H.304, L.305, L.306, E.315 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.291, E:L.305 Hydrogen bonds: E:S.303, E:L.305

1 x NDG- NAG- BMA- MAN- MAN- MAN- GLC- GLC- GLC- MAN- MAN: alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4: 24 residues within 4Å: Chain A: I.83, G.86, T.87, I.88, Y.89, R.329, I.346, N.544, N.545, T.546, W.547, N.548, T.550 Chain D: F.51, P.52, F.53, N.54 Chain H: Y.385, Y.418, E.419, I.422 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2, OTP.9, ZXT.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.346, A:Y.89 Hydrogen bonds: A:R.329, A:T.546, A:T.546, A:W.547, A:W.547, A:T.550, D:N.54, A:N.544

4 x KZB: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol(Non-covalent)

KZB.5: 7 residues within 4Å: Chain A: D.335, P.336, Y.398 Chain G: I.44, I.48, I.49, V.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.336, A:Y.398 KZB.6: 8 residues within 4Å: Chain A: I.129, V.130, H.133, E.137, F.174, Y.181, K.185, W.194 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.129, A:V.130, A:F.174, A:Y.181, A:W.194 Hydrogen bonds: A:E.137 KZB.11: 5 residues within 4Å: Chain F: L.587, Y.591 Chain H: M.436, L.437 Ligands: KZB.13 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:L.587, F:Y.591, F:Y.591, F:Y.591, H:M.436 KZB.13: 7 residues within 4Å: Chain F: L.550, W.594 Chain H: F.421, Y.426, A.430, F.433 Ligands: KZB.11 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: H:F.421, H:A.430, H:F.433, F:L.550, F:W.594 Hydrogen bonds: H:Y.426

2 x EGY: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium(Non-covalent)

EGY.7: 16 residues within 4Å: Chain A: L.221, L.224, V.225, T.229, R.231, F.379, L.382, I.387, M.391, M.397 Chain G: P.28, A.30, V.33, L.36, V.37, S.40 8 PLIP interactions: 2 interactions with chain G, 6 interactions with chain A Hydrophobic interactions: G:L.36, G:V.37, A:L.221, A:L.224, A:F.379, A:L.382, A:I.387 Salt bridges: A:R.231 EGY.12: 13 residues within 4Å: Chain A: F.65, Y.66, F.203, Y.204 Chain D: L.106, N.110 Chain F: Y.593, W.594, L.597, N.598, M.599 Chain H: H.415, R.420 9 PLIP interactions: 1 interactions with chain H, 6 interactions with chain A, 1 interactions with chain F, 1 interactions with chain D Salt bridges: H:H.415, A:H.69 Hydrophobic interactions: A:F.65, A:F.65, A:F.203, A:Y.204, D:L.106 Hydrogen bonds: A:Y.66, F:M.599

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

MN.8: 4 residues within 4Å: Chain A: D.49, D.167, N.168 Ligands: OTP.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.49, A:D.167, A:D.167

1 x OTP: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

OTP.9: 20 residues within 4Å: Chain A: N.168, W.209, G.210, G.211, F.214, N.217, L.224, G.272, V.273, W.326, F.330, L.333, L.334, T.395, F.399, R.405, L.406 Ligands: NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4, MN.8, ZXT.10 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.209, A:F.214, A:N.217, A:L.224, A:V.273, A:W.326, A:F.330, A:F.330, A:L.334, A:T.395, A:F.399, A:F.399, A:L.406 Hydrogen bonds: A:N.168, A:G.210 Salt bridges: A:R.405, A:R.405

1 x ZXT: 5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide

ZXT.10: 14 residues within 4Å: Chain A: Y.89, G.210, F.256, R.329, F.330, L.333, I.345, V.349, H.352, M.403, W.526 Ligands: NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4, NDG-NAG-BMA-MAN-MAN-MAN-GLC-GLC-GLC-MAN-MAN.4, OTP.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.330, A:L.333, A:I.345, A:V.349, A:W.526 Hydrogen bonds: A:Y.89, A:R.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lampson, B.L. et al., Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-kappa B. Cell (2024)

Release Date

2024-05-08

Peptides

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A: A
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4: B
Transmembrane protein 258: C
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1: D
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1: E
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2: F
Oligosaccharyltransferase complex subunit OSTC: G
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
G

Membrane

We predict this structure to be a membrane protein.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

Transmembrane protein 258

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

Oligosaccharyltransferase complex subunit OSTC

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

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