MolNFT v1 · #177169 · protein
Archaeal oligosaccharyltransferase aglb from archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate
7E9S · Dolichyl-phosphooligosaccharide-protein glycotransferase 3: “Archaeal oligosaccharyltransferase aglb from archaeoglobus fulgidus in complex with an inhibitory peptide and…”. X-ray diffraction, 3 ligands (7E8, J06, MN), 6 pockets…
- PDB
- 7E9S
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-phosphooligosaccharide-protein glycotransferase 3; A polypeptide linked to an…
- EC
- 2.4.99.21
- UniProt
- O29867
- Ligands
- 7E8, J06, MN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-phosphooligosaccharide-protein glycotransferase 3 (EC 2.4.99.21) | protein | 867 | 53% helix, 12% strand | O29867 |
| B | A polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- 7E8 · (2R)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate · ligand · 4 copies · chains A
- J06 · [(3S,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34Z,39S,43S)-3,7,11,15, 19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-6, 10,14,18,22,26,30,34-octaenyl] dihydrogen phosphate · ligand · chains A, B
- MN · Manganese (II) ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.76 | 0.78 | 98 | J06 |
| 2 | 278 | 0.56 | 0.76 | 25 | empty |
| 3 | 219 | 0.55 | 0.78 | 36 | PEG |
| 4 | 297 | 0.52 | 0.74 | 39 | empty |
| 5 | 215 | 0.48 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 7E9S · Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- O29867 · AlphaFold monomer V2.0 prediction for dolichyl- phosphooligosaccharide-protein… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O29867
- Elsewhere: RCSB PDB 7E9S · PDBe 7E9S · UniProt O29867
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