Research workbench
The cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
Analyse The cryo-EM structure of a eukaryotic oligosaccharyl transferase complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C26
- Type
- protein
- Length
- 2,077 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3…
- EC
- 2.4.99.18
- UniProt
- P39007, P41543, Q92316, Q99380, P46964, P48439, Q02795, P33767
- Ligands
- EGY, BMA, NAG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 8 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (EC 2.4.99.18) | protein | 648 | 48% helix, 5% strand | P39007 |
| 1 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (EC 2.4.99.18) | protein | 432 | 9% helix, 39% strand | P41543 |
| 5 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (EC 2.4.99.18) | protein | 84 | 68% helix, 1% strand | Q92316 |
| 4 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (EC 2.4.99.18) | protein | 34 | 82% helix, 0% strand | Q99380 |
| 2 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (EC 2.4.99.18) | protein | 108 | 78% helix, 0% strand | P46964 |
| 3 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 (EC 2.4.99.18) | protein | 126 | 64% helix, 0% strand | P48439 |
| C | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (EC 2.4.99.18) | protein | 248 | 30% helix, 14% strand | Q02795 |
| B | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (EC 2.4.99.18) | protein | 397 | 16% helix, 29% strand | P33767 |
Ligands and binding sites
- 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 · 8 copies · chains A, 1, C, 2, 5, 4, 3, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.76 | 0.78 | 82 | EGY |
| 2 | 357 | 0.74 | 0.85 | 45 | empty |
| 3 | 198 | 0.73 | 0.89 | 36 | empty |
| 4 | 71 | 0.72 | 0.96 | 23 | empty |
| 5 | 65 | 0.68 | 0.95 | 25 | empty |
Interfaces
14 interfaces between chains.
- C–B · 2630 Ų buried · 8 hydrogen bonds · protein-protein
- A–3 · 2377 Ų buried · 4 hydrogen bonds · protein-protein
- 1–5 · 1799 Ų buried · 6 hydrogen bonds · protein-protein
- A–4 · 1615 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1457 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 6C26 · The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex · the same entry in another collection · chain B against B, TM-score 1.00
- P41543 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain 1 against A, TM-score 0.96
- P46964 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain 2 against A, TM-score 0.94
- P39007 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A against A, TM-score 0.93
- P33767 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P39007
- Every structure of UniProt P41543
- Every structure of UniProt Q92316
- Every structure of UniProt Q99380
- Every structure of UniProt P46964
- Every structure of UniProt P48439
- Every structure of UniProt Q02795
- Every structure of UniProt P33767
- Elsewhere: RCSB PDB 6C26 · PDBe 6C26 · UniProt P39007 · UniProt P41543 · UniProt Q92316 · UniProt Q99380 · UniProt P46964 · UniProt P48439 · UniProt Q02795 · UniProt P33767
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