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Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AfAglB-S2, AF_0040, O30195_ARCFU) from Archaeoglobus fulgidus
Analyse Crystal structure of the C-terminal globular domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VU0
- Type
- protein
- Length
- 469 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Archaeoglobus fulgidus
- Molecule
- Putative uncharacterized protein
- EC
- 2.4.1.119
- UniProt
- O30195
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.94 · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein (EC 2.4.1.119) | protein | 153 | 46% helix, 16% strand | O30195 |
| B | Putative uncharacterized protein (EC 2.4.1.119) | protein | 162 | 45% helix, 16% strand | O30195 |
| C | Putative uncharacterized protein (EC 2.4.1.119) | protein | 154 | 45% helix, 15% strand | O30195 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.62 | 0.88 | 32 | empty |
| 2 | 61 | 0.28 | 0.73 | 11 | empty |
| 3 | 58 | 0.27 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 925 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3VU0 · Crystal structure of the C-terminal globular domain of oligosaccharyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- O30195 · AlphaFold monomer V2.0 prediction for dolichyl- phosphooligosaccharide-protein… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O30195
- Elsewhere: RCSB PDB 3VU0 · PDBe 3VU0 · UniProt O30195
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