MolNFT v1 · #187538 · protein
N-acetylglucosamine-1-phosphotransferase (gnpt) alpha and beta subunits (gnptab) catalytic domain, from zebrafish, in complex with uridine diphosphate N-acetylglucosamine (udp-glcnac) and magnesium
7SJ2 · N-acetylglucosamine-1-phosphotransferase subunit ALPHA,N…: “N-acetylglucosamine-1-phosphotransferase (gnpt) alpha and beta subunits (gnptab) catalytic domain, from…”. X-ray diffraction, 7 ligands (UD1, NAG, FUC), 12 pockets (best…
- PDB
- 7SJ2
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphotransferase subunit ALPHA,N…
- UniProt
- Q5RGJ8, Q54MP1
- Ligands
- UD1, NAG, FUC, BMA, MAN, MG, CA
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-1-phosphotransferase subunit ALPHA,N- acetylglucosamine-1-phosphotransferase (gnpt) alpha (gnptab) catalytic DOMAIN,N-acetylglucosamine-1-phosphotransferase subunit beta | protein | 428 | 44% helix, 15% strand | Q5RGJ8, Q54MP1 |
| B | N-acetylglucosamine-1-phosphotransferase subunit ALPHA,N- acetylglucosamine-1-phosphotransferase (gnpt) alpha (gnptab) catalytic DOMAIN,N-acetylglucosamine-1-phosphotransferase subunit beta | protein | 439 | 43% helix, 15% strand | Q5RGJ8, Q54MP1 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 4 copies · chains A, B
- 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 | 510 | 0.75 | 0.83 | 59 | MG, UD1 |
| 2 | 513 | 0.74 | 0.82 | 55 | MG, UD1 |
| 3 | 287 | 0.69 | 0.84 | 43 | empty |
| 4 | 99 | 0.57 | 0.86 | 22 | empty |
| 5 | 130 | 0.57 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2802 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SJ2 · 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 B against A, TM-score 0.95
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
- Every structure of UniProt Q54MP1
- Elsewhere: RCSB PDB 7SJ2 · PDBe 7SJ2 · UniProt Q5RGJ8 · UniProt Q54MP1
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