Research workbench
N-acetyl-B-D-glucosaminidase (gcna) from streptococcus gordonii
Analyse N-acetyl-B-D-glucosaminidase (gcna) from streptococcus gordonii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EPN
- Type
- protein
- Length
- 1,246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-beta-D-glucosaminidase
- EC
- 3.2.1.52
- UniProt
- Q6ST21
- Ligands
- NGT
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 623 | 51% helix, 13% strand | Q6ST21 |
Ligands and binding sites
- NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.65 | 0.80 | 46 | empty |
| 2 | 205 | 0.63 | 0.82 | 33 | NGT |
| 3 | 205 | 0.62 | 0.82 | 32 | NGT |
| 4 | 223 | 0.60 | 0.81 | 35 | empty |
| 5 | 109 | 0.49 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3705 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 2EPN · N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii · 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 Q6ST21
- Elsewhere: RCSB PDB 2EPN · PDBe 2EPN · UniProt Q6ST21
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