MolNFT v1 · #121270 · protein
A glycoside hydrolase family 97 enzyme (E480Q) in complex with panose from pseudoalteromonas sp. strain K8
5HQB · Alpha-glucosidase: “A glycoside hydrolase family 97 enzyme (E480Q) in complex with panose from pseudoalteromonas sp. strain K8”. X-ray diffraction, 5 ligands (GLC, CA, MG), 5 pockets (best druggability 0.76). MolNFT v1 #121270 on…
- PDB
- 5HQB
- Type
- protein
- Length
- 662 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- UniProt
- A0A0Y0DFX2
- Ligands
- GLC, CA, MG, CL, UNX
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase | protein | 662 | 18% helix, 37% strand | A0A0Y0DFX2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- UNX · Unknown atom or ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.76 | 0.96 | 25 | empty |
| 2 | 180 | 0.57 | 0.81 | 28 | GLC, GOL |
| 3 | 53 | 0.43 | 0.84 | 15 | empty |
| 4 | 127 | 0.38 | 0.74 | 21 | empty |
| 5 | 100 | 0.37 | 0.75 | 25 | empty |
Compared structures
- 5HQB · A Glycoside Hydrolase Family 97 enzyme (E480Q) in complex with Panose from… · 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 A0A0Y0DFX2
- Elsewhere: RCSB PDB 5HQB · PDBe 5HQB · UniProt A0A0Y0DFX2
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