Research workbench
Crystal structure of a transient covalent reaction intermediate of a family 51 alpha-L-arabinofuranosidase
Analyse Crystal structure of a transient covalent reaction intermediate of a family 51… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PZ2
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- Q9XBQ3
- Ligands
- AHR
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 497 | 29% helix, 27% strand | Q9XBQ3 |
Ligands and binding sites
- AHR · alpha-L-arabinofuranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.70 | 0.75 | 75 | empty |
| 2 | 248 | 0.55 | 0.77 | 38 | AHR |
| 3 | 175 | 0.50 | 0.77 | 29 | AHR |
| 4 | 180 | 0.48 | 0.77 | 37 | empty |
| 5 | 58 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1021 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 1PZ2 · Crystal structure of a transient covalent reaction intermediate of a family 51… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XBQ3 · AlphaFold monomer V2.0 prediction for intracellular exo… · 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 Q9XBQ3
- Elsewhere: RCSB PDB 1PZ2 · PDBe 1PZ2 · UniProt Q9XBQ3
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