Research workbench
Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from geobacillus thermoleovorans it-08 in complex with L-arabinose and D-xylose
Analyse Crystal structure of a thermostable glycoside hydrolase family 43… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z5I
- Type
- protein
- Length
- 504 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- Q2I2N4
- Ligands
- FUB, XYP, XYS, CA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylosidase (EC 3.2.1.37) | protein | 504 | 2% helix, 50% strand | Q2I2N4 |
Ligands and binding sites
- FUB · beta-L-arabinofuranose · ligand · chains A
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A
- XYS · alpha-D-xylopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.61 | 0.79 | 20 | empty |
| 2 | 194 | 0.56 | 0.80 | 36 | FUB, XYS |
| 3 | 123 | 0.45 | 0.78 | 18 | empty |
| 4 | 170 | 0.45 | 0.74 | 28 | empty |
Compared structures
- 5Z5I · Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase… · 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 Q2I2N4
- Elsewhere: RCSB PDB 5Z5I · PDBe 5Z5I · UniProt Q2I2N4
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