MolNFT v1 · #113145 · protein
GH20C, beta-hexosaminidase from streptococcus pneumoniae
5A6J · N-acetyl-beta-D-glucosaminidase: “GH20C, beta-hexosaminidase from streptococcus pneumoniae”. X-ray diffraction, 17 pockets (best druggability 0.71). MolNFT v1 #113145 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A6J
- Type
- protein
- Length
- 2,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-beta-D-glucosaminidase
- EC
- 3.2.1.52
- UniProt
- C1CH75
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 618 | 50% helix, 13% strand | C1CH75 |
| B | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 615 | 51% helix, 13% strand | C1CH75 |
| C | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 614 | 50% helix, 13% strand | C1CH75 |
| D | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 609 | 49% helix, 13% strand | C1CH75 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.71 | 0.77 | 57 | empty |
| 2 | 659 | 0.71 | 0.78 | 73 | empty |
| 3 | 390 | 0.61 | 0.77 | 45 | empty |
| 4 | 496 | 0.58 | 0.73 | 53 | empty |
| 5 | 335 | 0.57 | 0.76 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–C · 3360 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 211 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A6J · GH20C, Beta-hexosaminidase from Streptococcus pneumoniae · the same entry in another collection · chain B against B, 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 5A6J · PDBe 5A6J · UniProt C1CH75
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