MolNFT v1 · #147764 · protein
Crystal structure of full length endos from streptococcus pyogenes in complex with G2 oligosaccharide.
6EN3 · Endo-beta-N-acetylglucosaminidase F2,MULTIFUNCTIONAL…: “Crystal structure of full length endos from streptococcus pyogenes in complex with G2 oligosaccharide.”. X-ray diffraction, 6 ligands (NAG, MAN, GAL), 8 pockets (best…
- 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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