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Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofuranosidase from Streptomyces thermoviolaceus, bound to xylotetraose
Analyse Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofuranosidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O8P
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.557
- Source
- Streptomyces thermoviolaceus
- Molecule
- Alpha-L-arabinofuranosidase
- UniProt
- Q76BV4
- Ligands
- XYP, CA, K
- Pockets
- 1 · best druggability 0.44
Structure
x-ray diffraction · resolution 1.557 · 1 distinct chain · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-arabinofuranosidase | protein | 303 | 7% helix, 46% strand | Q76BV4 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- K · Potassium ion · metal · chains A
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.44 | 0.82 | 21 | XYP, K |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4O8P · Crystal structure of STHARAF62A, a GH62 family alpha-L- arabinofuranosidase from… · 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 Q76BV4
- Elsewhere: RCSB PDB 4O8P · PDBe 4O8P · UniProt Q76BV4
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