Research workbench
AgaD472N-Linear Blood group B type 2 trisaccharide complex structure
Analyse AgaD472N-Linear Blood group B type 2 trisaccharide complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PI0
- Type
- protein
- Length
- 721 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09
- Source
- Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- A0A0H2URQ6
- Ligands
- GAL, GLA
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · resolution 2.09 · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase (EC 3.2.1.22) | protein | 721 | 21% helix, 33% strand | A0A0H2URQ6 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains A
- GLA · alpha-D-galactopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- TLA · L(+)-tartaric acid · 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
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.49 | 0.83 | 21 | GAL, GLA |
| 2 | 155 | 0.44 | 0.75 | 29 | empty |
| 3 | 108 | 0.43 | 0.77 | 20 | EDO |
| 4 | 66 | 0.40 | 0.80 | 15 | EDO |
| 5 | 62 | 0.29 | 0.74 | 14 | empty |
Compared structures
- 6PI0 · AGAD472N-linear blood group B type 2 trisaccharide complex structure · 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 A0A0H2URQ6
- Elsewhere: RCSB PDB 6PI0 · PDBe 6PI0 · UniProt A0A0H2URQ6
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