Research workbench
Catalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence factor SpuA
Analyse Catalytic Module of the Multi-modular glycogen-degrading pneumococcal virulence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YA0
- Type
- protein
- Length
- 714 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- Putative alkaline amylopullulanase
- UniProt
- Q97SQ7
- Ligands
- NA, CA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · resolution 1.85 · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alkaline amylopullulanase | protein | 714 | 29% helix, 22% strand | Q97SQ7 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.57 | 0.78 | 35 | GOL, NA |
| 2 | 95 | 0.49 | 0.82 | 18 | GOL |
| 3 | 125 | 0.39 | 0.74 | 24 | empty |
| 4 | 50 | 0.36 | 0.80 | 14 | empty |
| 5 | 52 | 0.27 | 0.75 | 13 | CA |
Compared structures
- 2YA0 · Catalytic module of the multi-modular glycogen-degrading pneumococcal virulence factor… · 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 Q97SQ7
- Elsewhere: RCSB PDB 2YA0 · PDBe 2YA0 · UniProt Q97SQ7
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