Research workbench
Cryo-EM structure of yeast OST6P containing oligosaccharyltransferase complex
Analyse Cryo-EM structure of yeast OST6P containing oligosaccharyltransferase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OCI
- Type
- protein
- Length
- 2,095 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1…
- EC
- 2.4.99.18
- UniProt
- P41543, P46964, Q03723, Q99380, Q92316, P39007, P33767, Q02795
- Ligands
- PEE, AJP, V8K, NAG, MAN, BMA, MG
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 9 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (EC 2.4.99.18) | protein | 434 | 9% helix, 44% strand | P41543 |
| B | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (EC 2.4.99.18) | protein | 108 | 83% helix, 0% strand | P46964 |
| C | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 | protein | 119 | 65% helix, 3% strand | Q03723 |
| D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (EC 2.4.99.18) | protein | 35 | 83% helix, 0% strand | Q99380 |
| E | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (EC 2.4.99.18) | protein | 85 | 75% helix, 0% strand | Q92316 |
| F | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (EC 2.4.99.18) | protein | 639 | 56% helix, 5% strand | P39007 |
| G | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (EC 2.4.99.18) | protein | 393 | 20% helix, 30% strand | P33767 |
| H | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (EC 2.4.99.18) | protein | 258 | 32% helix, 21% strand | Q02795 |
| I | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1 (EC 2.4.99.18) | protein | 24 | 79% helix, 0% strand | — |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains A, E, F, B, C, D, G, H
- AJP · Digitonin · ligand · 2 copies · chains B, F, G, H, D, E
- V8K · Dolichylphosphate · ligand · chains B, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, F, G
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains G, H
- BMA · beta-D-mannopyranose · sugar · chains G
- MG · Magnesium ion · metal · chains F
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 | 855 | 0.74 | 0.78 | 78 | PEE |
| 2 | 132 | 0.72 | 0.91 | 28 | empty |
| 3 | 711 | 0.67 | 0.75 | 66 | PEE |
| 4 | 150 | 0.66 | 0.87 | 36 | empty |
| 5 | 422 | 0.59 | 0.75 | 44 | MG |
Interfaces
14 interfaces between chains.
- G–H · 2530 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 2275 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1953 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1620 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1578 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 7OCI · Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex · the same entry in another collection · chain I against I, TM-score 1.00
- P41543 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P46964 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain B against A, TM-score 0.96
- P39007 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain F against A, TM-score 0.95
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 P41543
- Every structure of UniProt P46964
- Every structure of UniProt Q03723
- Every structure of UniProt Q99380
- Every structure of UniProt Q92316
- Every structure of UniProt P39007
- Every structure of UniProt P33767
- Every structure of UniProt Q02795
- Elsewhere: RCSB PDB 7OCI · PDBe 7OCI · UniProt P41543 · UniProt P46964 · UniProt Q03723 · UniProt Q99380 · UniProt Q92316 · UniProt P39007 · UniProt P33767 · UniProt Q02795
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