Research workbench
Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus in complex with pentaerythritol propoxylate (5 4 po oh)
Analyse Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XVL
- 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
- PXN, NI, CL, SO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-xylosidase, putative, XYL31A (EC 3.2.1.-) | protein | 944 | 21% helix, 33% strand | B3PBD9 |
Ligands and binding sites
- PXN · (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol · ligand · chains A
- NI · Nickel (II) ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 7 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.71 | 0.98 | 22 | empty |
| 2 | 56 | 0.68 | 0.96 | 21 | empty |
| 3 | 101 | 0.65 | 0.90 | 23 | empty |
| 4 | 368 | 0.64 | 0.79 | 47 | PXN |
| 5 | 85 | 0.60 | 0.89 | 21 | empty |
Compared structures
- 2XVL · 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 2XVL · PDBe 2XVL · UniProt B3PBD9
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