Research workbench
Crystal structure of native ARA127N, a GH127 beta-L- arabinofuranosidase from geobacillus stearothermophilus T6
Analyse Crystal structure of native ARA127N, a GH127 beta-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
- 4QJY
- Type
- protein
- Length
- 1,274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH127 beta-L-arabinofuranosidase
- UniProt
- B3EYN9
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GH127 beta-L-arabinofuranosidase | protein | 637 | 40% helix, 20% strand | B3EYN9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.85 | 0.87 | 117 | ACT |
| 2 | 98 | 0.71 | 0.94 | 30 | ACT |
| 3 | 418 | 0.70 | 0.81 | 47 | ACT |
| 4 | 414 | 0.69 | 0.81 | 45 | ACT |
| 5 | 532 | 0.68 | 0.78 | 85 | ACT |
Interfaces
1 interface between chains.
- A–B · 2640 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4QJY · Crystal structure of native Ara127N, a GH127 beta-L-arabinofuranosidase from Geobacillus… · 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 B3EYN9
- Elsewhere: RCSB PDB 4QJY · PDBe 4QJY · UniProt B3EYN9
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