Research workbench
Crystal structure of TXGH116 (beta-glucosidase from thermoanaerobacterium xylolyticum) in complex with beta cyclophellitol cyclosulfate probe ME594
Analyse Crystal structure of TXGH116 (beta-glucosidase from thermoanaerobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NPF
- Type
- protein
- Length
- 763 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- F6BL85
- Ligands
- 945, CA
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 763 | 31% helix, 23% strand | F6BL85 |
Ligands and binding sites
- 945 · [(1~{R},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4, 5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate · ligand · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.53 | 0.79 | 26 | 945 |
| 2 | 97 | 0.38 | 0.75 | 20 | empty |
| 3 | 74 | 0.35 | 0.76 | 14 | empty |
| 4 | 69 | 0.35 | 0.77 | 23 | empty |
| 5 | 51 | 0.29 | 0.76 | 12 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5NPF · Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in… · 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 F6BL85
- Elsewhere: RCSB PDB 5NPF · PDBe 5NPF · UniProt F6BL85
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