MolNFT v1 · #81095 · protein
Crystal structure of a 6-SST/6-sft from pachysandra terminalis
3UGF · SUCROSE:(SUCROSE/FRUCTAN) 6-fructosyltransferase: “Crystal structure of a 6-SST/6-sft from pachysandra terminalis”. X-ray diffraction, 5 ligands (NAG, FUC, BMA), 12 pockets (best druggability 0.83). MolNFT v1 #81095 on GenesisL1: 3D…
- PDB
- 3UGF
- Type
- protein
- Length
- 1,054 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SUCROSE:(SUCROSE/FRUCTAN) 6-fructosyltransferase
- UniProt
- E3PQS3
- Ligands
- NAG, FUC, BMA, MAN, SO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SUCROSE:(SUCROSE/FRUCTAN) 6-fructosyltransferase | protein | 524 | 6% helix, 46% strand | E3PQS3 |
| B | SUCROSE:(SUCROSE/FRUCTAN) 6-fructosyltransferase | protein | 530 | 6% helix, 47% strand | E3PQS3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 13 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 | 1027 | 0.83 | 0.84 | 89 | GOL |
| 2 | 154 | 0.55 | 0.81 | 23 | empty |
| 3 | 179 | 0.53 | 0.78 | 26 | empty |
| 4 | 122 | 0.53 | 0.81 | 18 | empty |
| 5 | 154 | 0.51 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 3UGF · Crystal structure of a 6-SST/6-SFT from Pachysandra terminalis · 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 E3PQS3
- Elsewhere: RCSB PDB 3UGF · PDBe 3UGF · UniProt E3PQS3
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