Research workbench
Cryo-EM structure of human oligosaccharyltransferase complex ost-a
Analyse Cryo-EM structure of human oligosaccharyltransferase complex ost-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S7O
- Type
- protein
- Length
- 2,197 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A…
- EC
- 2.4.99.18
- UniProt
- P46977, P0C6T2, P61165, P61803, P04843, P04844, A0A024RAD5, Q9NRP0
- Ligands
- KZB, EGY, KZE, MAN, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A (EC 2.4.99.18) | protein | 656 | 57% helix, 5% strand | P46977 |
| B | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 | protein | 33 | 82% helix, 0% strand | P0C6T2 |
| C | Transmembrane protein 258 | protein | 78 | 73% helix, 3% strand | P61165 |
| D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 | protein | 110 | 81% helix, 0% strand | P61803 |
| E | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | protein | 560 | 25% helix, 33% strand | P04843 |
| F | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 | protein | 241 | 32% helix, 16% strand | P04844 |
| G | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit | protein | 411 | 18% helix, 27% strand | A0A024RAD5 |
| H | Oligosaccharyltransferase complex subunit ostc | protein | 108 | 68% helix, 0% strand | Q9NRP0 |
Ligands and binding sites
- 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 · ligand · 9 copies · chains A, D, E, F, G
- EGY · (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium · ligand · 7 copies · chains A, C, H, B, E, D, F, G
- KZE · [(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains F, G, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, G, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains G, E
- MG · Magnesium ion · metal · 2 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.81 | 0.84 | 60 | MG, KZE |
| 2 | 89 | 0.75 | 0.97 | 25 | empty |
| 3 | 791 | 0.73 | 0.78 | 67 | EGY |
| 4 | 596 | 0.68 | 0.77 | 74 | empty |
| 5 | 219 | 0.63 | 0.82 | 26 | EGY |
Interfaces
15 interfaces between chains.
- F–G · 2774 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 2223 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1916 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1619 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1517 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 6S7O · Cryo-EM structure of human oligosaccharyltransferase complex OST-A · the same entry in another collection · chain H against H, TM-score 1.00
- P46977 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9NRP0 · AlphaFold monomer V2.0 prediction for oligosaccharyltransferase complex subunit ostc… · a predicted model of the same protein · chain H against A, TM-score 0.94
- P61165 · AlphaFold monomer V2.0 prediction for transmembrane protein 258 (P61165) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P61803 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain D against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P46977
- Every structure of UniProt P0C6T2
- Every structure of UniProt P61165
- Every structure of UniProt P61803
- Every structure of UniProt P04843
- Every structure of UniProt P04844
- Every structure of UniProt A0A024RAD5
- Every structure of UniProt Q9NRP0
- Elsewhere: RCSB PDB 6S7O · PDBe 6S7O · UniProt P46977 · UniProt P0C6T2 · UniProt P61165 · UniProt P61803 · UniProt P04843 · UniProt P04844 · UniProt A0A024RAD5 · UniProt Q9NRP0
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