Research workbench
Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide and non-acceptor peptide bound
Analyse Structure of yeast oligosaccharylransferase complex with lipid-linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8AGC
- Type
- protein
- Length
- 2,151 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Saccharomyces cerevisiae; SYNTHETIC CONSTRUCT
- Molecule
- Dolichyl-diphosphooligosaccharide--protein glycotransferase; OST4 isoform 1…
- EC
- 2.4.99.18
- UniProt
- A0A6A5Q0M3, A0A8H8UM72, Q92316, A0A8H4BUV6, A0A6A5PXA1, A0A6V8S2Y6, A0A8H8ULL1, A0A6A5Q3S9
- Ligands
- CPL, PTY, ELU, 323, NAG, MAN, GLC, BMA, NDG, MN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 3.1 · 9 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycotransferase (EC 2.4.99.18) | protein | 697 | 61% helix, 5% strand | A0A6A5Q0M3 |
| B | OST4 isoform 1 | protein | 33 | 88% helix, 0% strand | A0A8H8UM72 |
| C | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 | protein | 85 | 73% helix, 2% strand | Q92316 |
| D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 | protein | 109 | 83% helix, 0% strand | A0A8H4BUV6 |
| E | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | protein | 438 | 10% helix, 47% strand | A0A6A5PXA1 |
| F | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 | protein | 258 | 31% helix, 18% strand | A0A6V8S2Y6 |
| G | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | protein | 394 | 21% helix, 33% strand | A0A8H8ULL1 |
| H | OST3 isoform 1 | protein | 131 | 62% helix, 0% strand | A0A6A5Q3S9 |
| P | Peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B, E, C, D, F, G
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, F, H
- ELU · phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate · ligand · chains A, P
- 323 · 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate · ligand · chains A, H, P
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, G, E
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains F, G, A
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, G, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains G, A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A, P
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.78 | 0.79 | 78 | NDG, NAG, ELU, MN |
| 2 | 1107 | 0.76 | 0.78 | 97 | GLC, PTY, CPL |
| 3 | 62 | 0.69 | 0.96 | 22 | empty |
| 4 | 464 | 0.69 | 0.80 | 54 | 323 |
| 5 | 179 | 0.69 | 0.87 | 42 | empty |
Interfaces
16 interfaces between chains.
- F–G · 2640 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 2403 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 1920 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 1653 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 covalent, 1 modified (N-glycosylation, covalent ligand, nonstandard).
Compared structures
- Q92316 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain C against A, TM-score 0.87
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 A0A6A5Q0M3
- Every structure of UniProt A0A8H8UM72
- Every structure of UniProt Q92316
- Every structure of UniProt A0A8H4BUV6
- Every structure of UniProt A0A6A5PXA1
- Every structure of UniProt A0A6V8S2Y6
- Every structure of UniProt A0A8H8ULL1
- Every structure of UniProt A0A6A5Q3S9
- Elsewhere: RCSB PDB 8AGC · PDBe 8AGC · UniProt A0A6A5Q0M3 · UniProt A0A8H8UM72 · UniProt Q92316 · UniProt A0A8H4BUV6 · UniProt A0A6A5PXA1 · UniProt A0A6V8S2Y6 · UniProt A0A8H8ULL1 · UniProt A0A6A5Q3S9
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