Research workbench
Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (phaglb-L, O74088_PYRHO) from pyrococcus horikoshii
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
- 3VU1
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0242
- EC
- 2.4.1.119
- UniProt
- O74088
- Ligands
- CA, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein PH0242 (EC 2.4.1.119) | protein | 488 | 16% helix, 48% strand | O74088 |
| B | Putative uncharacterized protein PH0242 (EC 2.4.1.119) | protein | 490 | 16% helix, 48% strand | O74088 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.84 | 0.85 | 94 | empty |
| 2 | 555 | 0.72 | 0.80 | 68 | empty |
| 3 | 399 | 0.68 | 0.80 | 35 | empty |
| 4 | 389 | 0.67 | 0.80 | 35 | empty |
| 5 | 120 | 0.54 | 0.83 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2016 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VU1 · Crystal structure of the C-terminal globular domain of oligosaccharyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- O74088 · AlphaFold monomer V2.0 prediction for dolichyl- phosphooligosaccharide-protein… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O74088
- Elsewhere: RCSB PDB 3VU1 · PDBe 3VU1 · UniProt O74088
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