MolNFT v1 · #115852 · protein
The structure of bacillus pumilus GH48 in complex with cellobiose and cellohexaose
5CVY · Glycoside hydrolase: “The structure of bacillus pumilus GH48 in complex with cellobiose and cellohexaose”. X-ray diffraction, 3 ligands (BGC, NA, CA), 3 pockets (best druggability 0.85). MolNFT v1 #115852 on GenesisL1: 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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