Research workbench
Crystal structure of beta-arabinopyranosidase
Analyse Crystal structure of beta-arabinopyranosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XFM
- Type
- protein
- Length
- 2,521 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- UniProt
- A0A1H5YQC4
- Ligands
- CA
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-glucosidase | protein | 632 | 21% helix, 35% strand | A0A1H5YQC4 |
| B | Alpha-glucosidase | protein | 628 | 21% helix, 35% strand | A0A1H5YQC4 |
| D | Alpha-glucosidase | protein | 629 | 21% helix, 35% strand | A0A1H5YQC4 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.79 | 0.84 | 88 | empty |
| 2 | 618 | 0.78 | 0.84 | 84 | empty |
| 3 | 542 | 0.70 | 0.80 | 40 | empty |
| 4 | 179 | 0.58 | 0.81 | 33 | CA |
| 5 | 179 | 0.57 | 0.81 | 36 | CA |
Interfaces
3 interfaces between chains.
- C–D · 1642 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1595 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 385 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5XFM · Crystal structure of beta-arabinopyranosidase · 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 A0A1H5YQC4
- Elsewhere: RCSB PDB 5XFM · PDBe 5XFM · UniProt A0A1H5YQC4
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