Research workbench
Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase
Analyse Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFA
- Type
- protein
- Length
- 1,403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase
- UniProt
- P71094
- Ligands
- EDT, NA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase | protein | 702 | 21% helix, 35% strand | P71094 |
| B | Alpha-glucosidase | protein | 701 | 21% helix, 35% strand | P71094 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.79 | 0.95 | 33 | empty |
| 2 | 104 | 0.78 | 0.98 | 32 | empty |
| 3 | 97 | 0.77 | 0.98 | 30 | empty |
| 4 | 143 | 0.77 | 0.95 | 33 | empty |
| 5 | 931 | 0.75 | 0.78 | 95 | EDT |
Interfaces
1 interface between chains.
- A–B · 1613 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3WFA · Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase · 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 P71094
- Elsewhere: RCSB PDB 3WFA · PDBe 3WFA · UniProt P71094
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