MolNFT v1 · #113327 · protein
GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with glcnac
5AC5 · N-acetyl-beta-D-glucosaminidase: “GH20C, beta-hexosaminidase from streptococcus pneumoniae in complex with glcnac”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.71). MolNFT v1 #113327 on GenesisL1: 3D structure…
- PDB
- 5AC5
- Type
- protein
- Length
- 1,235 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
- C1CH75
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 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 | 625 | 50% helix, 13% strand | C1CH75 |
| B | N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) | protein | 610 | 50% helix, 13% strand | C1CH75 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
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 | 483 | 0.71 | 0.81 | 60 | empty |
| 2 | 164 | 0.58 | 0.82 | 31 | NAG |
| 3 | 117 | 0.52 | 0.82 | 20 | NAG |
| 4 | 209 | 0.48 | 0.75 | 30 | empty |
| 5 | 221 | 0.47 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 3364 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 5AC5 · GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with GlcNAc · 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 5AC5 · PDBe 5AC5 · UniProt C1CH75
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