MolNFT v1 · #54650 · protein
Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus in complex with 5-fluoro-alpha-D-xylopyranosyl fluoride
2XVK · Alpha-xylosidase, putative, XYL31A: “Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus in complex with…”. X-ray diffraction, 3 ligands (FFX, NI, CL), 10 pockets (best druggability 0.70). MolNFT v1 #54650 on…
- PDB
- 2XVK
- Type
- protein
- Length
- 944 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-xylosidase, putative, XYL31A
- EC
- 3.2.1.-
- UniProt
- B3PBD9
- Ligands
- FFX, NI, CL
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-xylosidase, putative, XYL31A (EC 3.2.1.-) | protein | 944 | 21% helix, 34% strand | B3PBD9 |
Ligands and binding sites
- FFX · (2R,3S,5R,6S)-2,6-difluorooxane-3,4,5-triol · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.70 | 0.96 | 22 | empty |
| 2 | 96 | 0.67 | 0.91 | 19 | empty |
| 3 | 87 | 0.63 | 0.90 | 23 | empty |
| 4 | 254 | 0.57 | 0.78 | 38 | FFX |
| 5 | 203 | 0.49 | 0.76 | 29 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2XVK · crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with… · 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 B3PBD9
- Elsewhere: RCSB PDB 2XVK · PDBe 2XVK · UniProt B3PBD9
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