8PN9: Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1

PDB ID: 8PN9Download
MMDB ID: 246451
PDB Deposition Date: 2023/6/30
Updated in MMDB: 2024/05
Experimental Method:
electron microscopy
Resolution: 3.61  Å
Source Organism:
Similar Structures:
Biological Unit for 8PN9: octameric; determined by author
Molecular Components in 8PN9
Label Count Molecule
Proteins (8 molecules)
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase Subunit Stt3a
(Gene symbol: STT3A)
Molecule annotation
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase Subunit 4
(Gene symbol: OST4)
Molecule annotation
1
Transmembrane Protein 258
(Gene symbol: TMEM258)
Molecule annotation
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase Subunit Dad1
(Gene symbol: DAD1)
Molecule annotation
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase Subunit 1
(Gene symbol: RPN1)
Molecule annotation
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase Subunit 2
(Gene symbol: RPN2)
Molecule annotation
1
Oligosaccharyltransferase Complex Subunit Ostc
(Gene symbol: OSTC)
Molecule annotation
1
Dolichyl-diphosphooligosaccharide--protein Glycosyltransferase 48 KDA Subunit
(Gene symbol: DDOST)
Molecule annotation
Chemicals and Non-standard biopolymers (37 molecules)
1
7
2-acetamido-2-deoxy-beta-D-glucopyranose2-acetamido-2-deoxy-beta-D-glucopyranose
2
3
beta-D-mannopyranosebeta-D-mannopyranose
3
14
alpha-D-mannopyranosealpha-D-mannopyranose
4
1
2-acetamido-2-deoxy-alpha-D-glucopyranose2-acetamido-2-deoxy-alpha-D-glucopyranose
5
3
alpha-D-glucopyranosealpha-D-glucopyranose
6
4
(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(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
7
2
(4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium(4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium
8
1
MANGANESE (II) IONMANGANESE (II) ION
9
1
(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(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
10
1
5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303