MolNFT v1 · #156734 · protein
Crystal structure of streptococcus pyogenes endo-beta-N- acetylglucosaminidase (ENDOS2) with complex biantennary glycan
6MDS · Endo-beta-N-acetylglucosaminidase: “Crystal structure of streptococcus pyogenes endo-beta-N- acetylglucosaminidase (ENDOS2) with complex…”. X-ray diffraction, 5 ligands (NAG, MAN, GAL), 9 pockets (best druggability 0.57). MolNFT v1…
- PDB
- 6MDS
- Type
- protein
- Length
- 1,574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase
- UniProt
- T1WGN1
- Ligands
- NAG, MAN, GAL, BMA, CA
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.57 | 0.80 | 38 | empty |
| 2 | 135 | 0.52 | 0.81 | 32 | empty |
| 3 | 229 | 0.48 | 0.74 | 33 | NAG, BMA, MAN |
| 4 | 181 | 0.45 | 0.74 | 31 | NAG, MAN |
| 5 | 106 | 0.39 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6MDS · 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 6MDS · PDBe 6MDS · UniProt T1WGN1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.