Research workbench
Crystal structure of C. jejuni pglb C-terminal domain
Analyse Crystal structure of C. jejuni pglb C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AAG
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General glycosylation pathway protein
- UniProt
- Q5HTX9
- Ligands
- CA
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General glycosylation pathway protein | protein | 267 | 33% helix, 23% strand | Q5HTX9 |
| B | General glycosylation pathway protein | protein | 236 | 30% helix, 27% strand | Q5HTX9 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.77 | 0.80 | 75 | empty |
| 2 | 77 | 0.52 | 0.84 | 22 | empty |
| 3 | 125 | 0.43 | 0.76 | 22 | empty |
| 4 | 66 | 0.31 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 684 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (methylation, engineered).
Compared structures
- 3AAG · Crystal structure of C. jejuni pglb C-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HTX9 · AlphaFold monomer V2.0 prediction for undecaprenyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A 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 Q5HTX9
- Elsewhere: RCSB PDB 3AAG · PDBe 3AAG · UniProt Q5HTX9
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