Research workbench
Beta-primeverosidase in complex with disaccharide substrate-analog N- beta-primeverosylamidine, natural 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
- 3WQ5
- 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
- VPA, NAG, BMA
- Pockets
- 6 · 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, 18% strand | Q7X9A9 |
| B | Beta-primeverosidase (EC 3.2.1.149) | protein | 474 | 46% helix, 18% strand | Q7X9A9 |
Ligands and binding sites
- VPA · 2-phenyl-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)ethylamidine · ligand · 3 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.76 | 0.84 | 42 | VPA |
| 2 | 441 | 0.75 | 0.84 | 39 | VPA |
| 3 | 304 | 0.51 | 0.74 | 32 | empty |
| 4 | 71 | 0.36 | 0.77 | 14 | empty |
| 5 | 64 | 0.34 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WQ5 · beta-Primeverosidase in complex with disaccharide substrate-analog… · the same entry in another collection · chain B against B, 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 3WQ5 · PDBe 3WQ5 · UniProt Q7X9A9
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