Research workbench
N-acetylglucosamine-1-phosphotransferase (gnpt) gamma subunit (gnptg), from clawed frog
Analyse N-acetylglucosamine-1-phosphotransferase (gnpt) gamma subunit (gnptg), from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S69
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphotransferase gamma subunit
- UniProt
- Q68F17
- Ligands
- MAN, NAG, BMA, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylglucosamine-1-phosphotransferase gamma subunit | protein | 174 | 24% helix, 36% strand | Q68F17 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 9 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CL · Chloride ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.47 | 0.75 | 28 | empty |
| 2 | 62 | 0.39 | 0.80 | 14 | CL |
| 3 | 50 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7S69 · N-acetylglucosamine-1-phosphotransferase (GNPT) gamma subunit (GNPTG), from clawed frog · 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 Q68F17
- Elsewhere: RCSB PDB 7S69 · PDBe 7S69 · UniProt Q68F17
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