Research workbench
Crystal structure of a cell-wall invertase (D23A) from arabidopsis thaliana in complex with sucrose
Analyse Crystal structure of a cell-wall invertase (D23A) from arabidopsis thaliana in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQW
- Type
- protein
- Length
- 534 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-fructofuranosidase
- EC
- 3.2.1.26
- UniProt
- Q43866
- Ligands
- NAG, MAN, GLC, FRU, ZN
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-fructofuranosidase (EC 3.2.1.26) | protein | 534 | 5% helix, 47% strand | Q43866 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- ZN · Zinc ion · metal · 4 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.52 | 0.84 | 24 | empty |
| 2 | 237 | 0.51 | 0.75 | 33 | empty |
| 3 | 165 | 0.51 | 0.78 | 29 | NAG, GLC, FRU |
| 4 | 92 | 0.41 | 0.77 | 18 | ZN |
| 5 | 53 | 0.30 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 2QQW · Crystal structure of a cell-wall invertase (D23A) from Arabidopsis thaliana in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q43866 · AlphaFold monomer V2.0 prediction for beta-fructofuranosidase, insoluble isoenzyme CWINV1… · a predicted model of the same protein · 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 Q43866
- Elsewhere: RCSB PDB 2QQW · PDBe 2QQW · UniProt Q43866
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