MolNFT v1 · #148194 · protein
Cryo-EM structure of the yeast oligosaccharyltransferase (ost) complex
6EZN · Dolichyl-diphosphooligosaccharide--protein…: “Cryo-EM structure of the yeast oligosaccharyltransferase (ost) complex”. Electron microscopy, 5 ligands (CPL, PTY, NAG), 20 pockets (best druggability 0.77). MolNFT v1 #148194 on…
- PDB
- 6EZN
- Type
- protein
- Length
- 2,090 residues
- Chains
- 8
- 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, P48439, Q99380, Q92316, P39007, P33767, Q02795
- Ligands
- CPL, PTY, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 8 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (EC 2.4.99.18) | protein | 438 | 8% helix, 44% strand | P41543 |
| B | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (EC 2.4.99.18) | protein | 110 | 80% helix, 0% strand | P46964 |
| C | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 (EC 2.4.99.18) | protein | 120 | 65% helix, 0% strand | P48439 |
| D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (EC 2.4.99.18) | protein | 34 | 82% helix, 0% strand | Q99380 |
| E | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (EC 2.4.99.18) | protein | 85 | 65% helix, 2% strand | Q92316 |
| F | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (EC 2.4.99.18) | protein | 650 | 53% helix, 4% strand | P39007 |
| G | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (EC 2.4.99.18) | protein | 394 | 18% helix, 31% strand | P33767 |
| H | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (EC 2.4.99.18) | protein | 259 | 29% helix, 15% strand | Q02795 |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, E, F, D, B, G, H
- PTY · Phosphatidylethanolamine · ligand · chains F, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, F, G
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains G, H
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains G
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 | 1034 | 0.77 | 0.78 | 81 | PTY, CPL |
| 2 | 671 | 0.65 | 0.75 | 65 | CPL |
| 3 | 483 | 0.63 | 0.76 | 55 | empty |
| 4 | 96 | 0.60 | 0.87 | 16 | empty |
| 5 | 180 | 0.59 | 0.82 | 45 | empty |
Interfaces
14 interfaces between chains.
- G–H · 2596 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 2379 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1903 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1641 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1639 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 6EZN · Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex · the same entry in another collection · chain H against H, 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
- P33767 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain G against A, TM-score 0.94
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 P48439
- 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 6EZN · PDBe 6EZN · UniProt P41543 · UniProt P46964 · UniProt P48439 · UniProt Q99380 · UniProt Q92316 · UniProt P39007 · UniProt P33767 · UniProt Q02795
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