Research workbench
Crystal structure of full length endos from streptococcus pyogenes in complex with G2 oligosaccharide.
Analyse Crystal structure of full length endos from streptococcus pyogenes in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EN3
- Type
- protein
- Length
- 934 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase F2,MULTIFUNCTIONAL- autoprocessing repeats-in-toxin
- EC
- 3.4.22.-, 6.3.2.-
- UniProt
- J7M8R4, Q9KS12
- Ligands
- NAG, MAN, GAL, BMA, CA, NI
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase F2,MULTIFUNCTIONAL- autoprocessing repeats-in-toxin (EC 3.4.22.-, 6.3.2.-) | protein | 934 | 30% helix, 21% strand | J7M8R4, Q9KS12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
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 | 605 | 0.66 | 0.76 | 59 | NAG, BMA, MAN |
| 2 | 241 | 0.54 | 0.77 | 45 | empty |
| 3 | 132 | 0.47 | 0.78 | 20 | empty |
| 4 | 114 | 0.39 | 0.75 | 19 | empty |
| 5 | 97 | 0.33 | 0.73 | 16 | empty |
Compared structures
- 6EN3 · Crystal structure of full length EndoS from Streptococcus pyogenes in complex with G2… · 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 J7M8R4
- Every structure of UniProt Q9KS12
- Elsewhere: RCSB PDB 6EN3 · PDBe 6EN3 · UniProt J7M8R4 · UniProt Q9KS12
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