MolNFT v1 · #137361 · protein
Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine
5VMA · Glycoside hydrolase: “Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine”. X-ray diffraction, 4 ligands (G2I, 9MR, CA), 3 pockets (best druggability 0.85). MolNFT v1 #137361 on GenesisL1: 3D structure…
- PDB
- 5VMA
- Type
- protein
- Length
- 700 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- UniProt
- A8FDC4
- Ligands
- G2I, 9MR, CA, NA
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase | protein | 700 | 36% helix, 18% strand | A8FDC4 |
Ligands and binding sites
- G2I · (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 2 copies · chains A
- 9MR · (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 12 copies · chains A
- MLI · Malonate ion · additive · chains A
- ACT · Acetate ion · additive · 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 | 1152 | 0.85 | 0.86 | 105 | G2I, 9MR, EDO |
| 2 | 52 | 0.35 | 0.79 | 19 | EDO |
| 3 | 59 | 0.27 | 0.72 | 12 | EDO |
Compared structures
- 5VMA · Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine · 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 5VMA · PDBe 5VMA · UniProt A8FDC4
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