Research workbench
The structure of bacillus pumilus GH48 in complex with cellobiose and cellohexaose
Analyse The structure of bacillus pumilus GH48 in complex with cellobiose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CVY
- Type
- protein
- Length
- 701 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A8FDC4
- Ligands
- BGC, NA, CA
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 701 | 37% helix, 18% strand | A8FDC4 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A
- NA · Sodium ion · metal · 15 copies · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- MLI · Malonate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.85 | 0.86 | 109 | BGC, MLI, EDO, GOL, NA |
| 2 | 50 | 0.26 | 0.74 | 15 | empty |
| 3 | 55 | 0.26 | 0.73 | 12 | empty |
Compared structures
- 5CVY · The Structure of Bacillus pumilus GH48 in complex with cellobiose and cellohexaose · 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 A8FDC4
- Elsewhere: RCSB PDB 5CVY · PDBe 5CVY · UniProt A8FDC4
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