Research workbench
Structure of the E242A mutant of the alpha-L-arabinofuranosidase ARB93A from fusarium graminearum in complex with an iminosugar inhibitor
Analyse Structure of the E242A mutant of the alpha-L-arabinofuranosidase ARB93A from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDP
- Type
- protein
- Length
- 1,079 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-1,5-alpha-L-arabinofuranobiosidase
- EC
- 3.2.1.55
- UniProt
- B8ZY56
- Ligands
- EDG, AHR, CA
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-1,5-alpha-L-arabinofuranobiosidase (EC 3.2.1.55) | protein | 361 | 1% helix, 45% strand | B8ZY56 |
| B, C | Exo-1,5-alpha-L-arabinofuranobiosidase (EC 3.2.1.55) | protein | 359 | 1% helix, 44% strand | B8ZY56 |
Ligands and binding sites
- EDG · 1,4-dideoxy-1,4-imino-L-arabinitol · ligand · 3 copies · chains A, B, C
- AHR · alpha-L-arabinofuranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.72 | 0.81 | 32 | empty |
| 2 | 647 | 0.71 | 0.79 | 67 | empty |
| 3 | 479 | 0.71 | 0.80 | 29 | empty |
| 4 | 444 | 0.70 | 0.80 | 29 | empty |
| 5 | 521 | 0.67 | 0.78 | 50 | empty |
Interfaces
2 interfaces between chains.
- A–B · 730 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 718 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2YDP · Structure of the E242A mutant of the alpha-l-arabinofuranosidase arb93a from fusarium… · 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 B8ZY56
- Elsewhere: RCSB PDB 2YDP · PDBe 2YDP · UniProt B8ZY56
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