MolNFT v1 · #52130 · protein
Structure of an inactive mutant of arabinofuranosidase from thermobacillus xylanilyticus in complex with a pentasaccharide
2VRQ · Alpha-L-arabinofuranosidase: “Structure of an inactive mutant of arabinofuranosidase from thermobacillus xylanilyticus in complex with a…”. X-ray diffraction, 3 ligands (XYP, AHR, PO4), 10 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 2VRQ
- Type
- protein
- Length
- 1,479 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase
- EC
- 3.2.1.55
- UniProt
- O69262
- Ligands
- XYP, AHR, PO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-L-arabinofuranosidase (EC 3.2.1.55) | protein | 493 | 30% helix, 30% strand | O69262 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A, B, C
- AHR · alpha-L-arabinofuranose · sugar · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.83 | 0.84 | 86 | empty |
| 2 | 130 | 0.71 | 0.91 | 21 | empty |
| 3 | 131 | 0.71 | 0.91 | 19 | empty |
| 4 | 85 | 0.42 | 0.78 | 23 | XYP, AHR |
| 5 | 105 | 0.40 | 0.76 | 22 | XYP, AHR |
Interfaces
3 interfaces between chains.
- A–C · 905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 852 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VRQ · Structure of an inactive mutant of arabinofuranosidase from thermobacillus xylanilyticus… · 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 O69262
- Elsewhere: RCSB PDB 2VRQ · PDBe 2VRQ · UniProt O69262
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