Research workbench
Beta-primeverosidase in complex with disaccharide substrate-analog N- beta-primeverosylamidine, artificial aglycone derivative
Analyse Beta-primeverosidase in complex with disaccharide substrate-analog N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WQ6
- Type
- protein
- Length
- 949 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-primeverosidase
- EC
- 3.2.1.149
- UniProt
- Q7X9A9
- Ligands
- ZPA, NAG, BMA, FUC
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-primeverosidase (EC 3.2.1.149) | protein | 475 | 46% helix, 17% strand | Q7X9A9 |
| B | Beta-primeverosidase (EC 3.2.1.149) | protein | 474 | 46% helix, 18% strand | Q7X9A9 |
Ligands and binding sites
- ZPA · 4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.76 | 0.84 | 37 | ZPA |
| 2 | 457 | 0.75 | 0.84 | 41 | ZPA |
| 3 | 63 | 0.36 | 0.78 | 15 | empty |
| 4 | 70 | 0.35 | 0.77 | 15 | empty |
| 5 | 124 | 0.35 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WQ6 · beta-Primeverosidase in complex with disaccharide substrate-analog… · 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 Q7X9A9
- Elsewhere: RCSB PDB 3WQ6 · PDBe 3WQ6 · UniProt Q7X9A9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.