Research workbench
Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2) with high-mannose glycan
Analyse Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MDV
- Type
- protein
- Length
- 1,574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Streptococcus pyogenes
- Molecule
- Endo-beta-N-acetylglucosaminidase
- UniProt
- T1WGN1
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 12 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-beta-N-acetylglucosaminidase | protein | 787 | 28% helix, 25% strand | T1WGN1 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CA · Calcium 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.51 | 0.79 | 29 | empty |
| 2 | 119 | 0.47 | 0.79 | 29 | empty |
| 3 | 181 | 0.47 | 0.75 | 32 | empty |
| 4 | 181 | 0.45 | 0.74 | 32 | NAG |
| 5 | 139 | 0.45 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6MDV · Crystal structure of streptococcus pyogenes endo-beta-N- acetylglucosaminidase (ENDOS2)… · 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 T1WGN1
- Elsewhere: RCSB PDB 6MDV · PDBe 6MDV · UniProt T1WGN1
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