Research workbench
N-acetylglucosamine-1-phosphotransferase (gnpt) alpha and beta subunits (gnptab) catalytic domain, from zebrafish
Analyse N-acetylglucosamine-1-phosphotransferase (gnpt) alpha and beta subunits… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6N
- Type
- protein
- Length
- 868 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphotransferase (gnpt) alpha (gnptab) catalytic…
- UniProt
- Q5RGJ8
- Ligands
- NAG, BMA, FUC, MAN, CA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-1-phosphotransferase (gnpt) alpha (gnptab) catalytic DOMAIN,N-acetylglucosamine-1-phosphotransferase subunit beta | protein | 422 | 44% helix, 16% strand | Q5RGJ8 |
| B | N-acetylglucosamine-1-phosphotransferase (gnpt) alpha (gnptab) catalytic DOMAIN,N-acetylglucosamine-1-phosphotransferase subunit beta | protein | 446 | 43% helix, 15% strand | Q5RGJ8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.74 | 0.78 | 70 | empty |
| 2 | 533 | 0.71 | 0.80 | 58 | empty |
| 3 | 228 | 0.69 | 0.86 | 34 | empty |
| 4 | 98 | 0.58 | 0.86 | 16 | empty |
| 5 | 112 | 0.58 | 0.85 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2789 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 7S6N · N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5RGJ8 · AlphaFold monomer V2.0 prediction for N-acetylglucosamine-1-phosphotransferase subunits… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q5RGJ8
- Elsewhere: RCSB PDB 7S6N · PDBe 7S6N · UniProt Q5RGJ8
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