Research workbench
GH127 beta-L-arabinofuranosidase HYPBA1 covalently complexed with alpha-L-arabinofuranosylamide
Analyse GH127 beta-L-arabinofuranosidase HYPBA1 covalently complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EXW
- Type
- protein
- Length
- 644 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-reducing end beta-L-arabinofuranosidase
- EC
- 3.2.1.185
- UniProt
- E8MGH8
- Ligands
- 09X, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-reducing end beta-L-arabinofuranosidase (EC 3.2.1.185) | protein | 644 | 40% helix, 18% strand | E8MGH8 |
Ligands and binding sites
- 09X · 2-bromanyl-N-[(2R,3R,4R,5S}-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.67 | 0.80 | 42 | empty |
| 2 | 334 | 0.62 | 0.78 | 39 | 09X |
| 3 | 346 | 0.60 | 0.77 | 33 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EXW · GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- E8MGH8 · AlphaFold monomer V2.0 prediction for non-reducing end beta-L- arabinofuranosidase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 E8MGH8
- Elsewhere: RCSB PDB 7EXW · PDBe 7EXW · UniProt E8MGH8
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