Research workbench
Crystal structure of mouse peptide N-glycanase C-terminal domain in complex with mannopentaose
Analyse Crystal structure of mouse peptide N-glycanase C-terminal domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I74
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pngase
- EC
- 3.5.1.52
- UniProt
- Q9JI78
- Ligands
- MAN
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pngase (EC 3.5.1.52) | protein | 180 | 11% helix, 51% strand | Q9JI78 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.56 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2I74 · Crystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JI78 · AlphaFold monomer V2.0 prediction for peptide-N(4)-(N-acetyl-beta… · 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 Q9JI78
- Elsewhere: RCSB PDB 2I74 · PDBe 2I74 · UniProt Q9JI78
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