Research workbench
Crystal structure of streptococcus pyogenes endo-beta-N- acetylglucosaminidase (ENDOS2)
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
- 6E58
- Type
- protein
- Length
- 1,573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted endo-beta-N-acetylglucosaminidase (endos)
- UniProt
- A0A0H3C1U3
- Ligands
- CA
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secreted endo-beta-N-acetylglucosaminidase (endos) | protein | 787 | 27% helix, 26% strand | A0A0H3C1U3 |
| B | Secreted endo-beta-N-acetylglucosaminidase (endos) | protein | 786 | 28% helix, 26% strand | A0A0H3C1U3 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.52 | 0.80 | 33 | empty |
| 2 | 113 | 0.52 | 0.82 | 28 | empty |
| 3 | 221 | 0.48 | 0.74 | 38 | empty |
| 4 | 89 | 0.39 | 0.77 | 25 | empty |
| 5 | 99 | 0.37 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 394 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6E58 · 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 A0A0H3C1U3
- Elsewhere: RCSB PDB 6E58 · PDBe 6E58 · UniProt A0A0H3C1U3
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