Research workbench
Recombinant peptide: N-glycanase F (pngase F)
Analyse Recombinant peptide: N-glycanase F (pngase F) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PMS
- Type
- protein
- Length
- 312 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PEPTIDE:N-glycosidase F
- EC
- 3.5.1.52
- UniProt
- Q9XBM8
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PEPTIDE:N-glycosidase F (EC 3.5.1.52) | protein | 312 | 5% helix, 47% strand | Q9XBM8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 10 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.50 | 0.81 | 20 | GOL |
| 2 | 86 | 0.33 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3PMS · Recombinant peptide: N-glycanase F (PNGase F) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9XBM8
- Elsewhere: RCSB PDB 3PMS · PDBe 3PMS · UniProt Q9XBM8
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