Research workbench
GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with GalNAc
Analyse GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with GalNAc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AC4
- Type
- protein
- Length
- 1,250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.08
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- N-acetyl-beta-D-glucosaminidase
- EC
- 3.2.1.52
- UniProt
- C1CH75
- Ligands
- NGA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.08 · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 625 | 49% helix, 13% strand | C1CH75 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.77 | 0.81 | 94 | NGA |
| 2 | 135 | 0.56 | 0.82 | 31 | empty |
| 3 | 79 | 0.51 | 0.84 | 13 | NGA |
| 4 | 189 | 0.44 | 0.74 | 28 | empty |
| 5 | 174 | 0.44 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3404 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 5AC4 · GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with galnac · 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 C1CH75
- Elsewhere: RCSB PDB 5AC4 · PDBe 5AC4 · UniProt C1CH75
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