Research workbench
Crystal structure of a GH43 arabonofuranosidase from weissella sp. strain 142
Analyse Crystal structure of a GH43 arabonofuranosidase from weissella sp. strain 142 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M8E
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- A0A0D1M7L2
- Ligands
- CA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-N-arabinofuranosidase (EC 3.2.1.55) | protein | 323 | 5% helix, 46% strand | A0A0D1M7L2 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.74 | 0.82 | 71 | empty |
| 2 | 285 | 0.72 | 0.85 | 32 | GOL |
| 3 | 305 | 0.72 | 0.84 | 35 | GOL |
| 4 | 328 | 0.60 | 0.78 | 33 | empty |
| 5 | 279 | 0.59 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1559 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5M8E · Crystal structure of a GH43 arabonofuranosidase from Weissella sp. strain 142 · 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 A0A0D1M7L2
- Elsewhere: RCSB PDB 5M8E · PDBe 5M8E · UniProt A0A0D1M7L2
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