MolNFT v1 · #113146 · protein
GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with gal-ngt
5A6K: “GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with gal-ngt”. X-ray diffraction, 1 ligand (NSG), 6 pockets (best druggability 0.77). MolNFT v1 #113146 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5A6K
- Type
- protein
- Length
- 1,251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH20C
- EC
- 3.2.1.52
- UniProt
- C1CH75
- Ligands
- NSG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH20C (EC 3.2.1.52) | protein | 626 | 49% helix, 13% strand | C1CH75 |
| B | GH20C (EC 3.2.1.52) | protein | 625 | 50% helix, 13% strand | C1CH75 |
Ligands and binding sites
- NSG · (2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.77 | 0.79 | 106 | NSG |
| 2 | 298 | 0.62 | 0.79 | 52 | empty |
| 3 | 202 | 0.46 | 0.74 | 30 | empty |
| 4 | 117 | 0.39 | 0.74 | 20 | empty |
| 5 | 70 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3377 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 5A6K · GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT · 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 5A6K · PDBe 5A6K · UniProt C1CH75
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