Research workbench
Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, strh
Analyse Differential inhibition of the tandem GH20 catalytic modules in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AZI
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- P49610
- Ligands
- BCN, OAN, BR
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 410 | 43% helix, 18% strand | P49610 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 408 | 43% helix, 18% strand | P49610 |
Ligands and binding sites
- BCN · Bicine · ligand · 3 copies · chains A, B
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.85 | 0.86 | 99 | OAN, EDO, BR |
| 2 | 305 | 0.57 | 0.77 | 43 | OAN, EDO, BCN |
| 3 | 143 | 0.43 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1009 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4AZI · Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal… · the same entry in another collection · chain A against A, TM-score 1.00
- P49610 · AlphaFold monomer V2.0 prediction for beta-N-acetylhexosaminidase (P49610) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P49610
- Elsewhere: RCSB PDB 4AZI · PDBe 4AZI · UniProt P49610
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