Research workbench
Crystal structure of the archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the nvt sequon via a disulfide bond
Analyse Crystal structure of the archaeoglobus fulgidus oligosaccharyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMY
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane oligosaccharyl transferase, putative; Acceptor peptide…
- EC
- 2.4.99.18
- UniProt
- O29867
- Ligands
- MG
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane oligosaccharyl transferase, putative (EC 2.4.99.18) | protein | 848 | 50% helix, 11% strand | O29867 |
| B | Acceptor peptide, arg-tyr-asn-val-thr-ala-cys | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.55 | 0.76 | 26 | empty |
| 2 | 239 | 0.53 | 0.76 | 32 | empty |
| 3 | 273 | 0.50 | 0.74 | 42 | empty |
| 4 | 184 | 0.46 | 0.74 | 19 | empty |
| 5 | 177 | 0.46 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5GMY · Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU)… · 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 5GMY · PDBe 5GMY · UniProt O29867
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