MolNFT v1 · #189486 · protein
Crystal structure of GH3 beta-N-acetylhexosaminidase AMUC_2109 from akkermansia muciniphila in complex with glcnac
7VI7: “Crystal structure of GH3 beta-N-acetylhexosaminidase AMUC_2109 from akkermansia muciniphila in complex with…”. X-ray diffraction, 3 ligands (NDG, MG, CL), 8 pockets (best druggability 0.64). MolNFT v1 #189486 on GenesisL1: 3D…
- PDB
- 7VI7
- Type
- protein
- Length
- 681 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
- B2UPP0
- Ligands
- NDG, MG, CL
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 342 | 49% helix, 13% strand | B2UPP0 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 339 | 50% helix, 13% strand | B2UPP0 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.64 | 0.79 | 43 | CL |
| 2 | 435 | 0.61 | 0.76 | 51 | NDG |
| 3 | 360 | 0.58 | 0.76 | 48 | NDG, MG |
| 4 | 77 | 0.53 | 0.85 | 22 | empty |
| 5 | 80 | 0.51 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7VI7 · Crystal structure of GH3 beta-N-acetylhexosaminidase Amuc_2109 from Akkermansia… · 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 B2UPP0
- Elsewhere: RCSB PDB 7VI7 · PDBe 7VI7 · UniProt B2UPP0
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