MolNFT v1 · #153811 · protein
Crystallization analysis of a beta-N-acetylhexosaminidase (AM2136) from akkermansia muciniphila
6JQF · Glycoside hydrolase, family 20, catalytic core: “Crystallization analysis of a beta-N-acetylhexosaminidase (AM2136) from akkermansia muciniphila”. X-ray diffraction, 3 ligands (NAG, MG, CL), 6 pockets (best druggability 0.58).…
- PDB
- 6JQF
- Type
- protein
- Length
- 734 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase, family 20, catalytic core
- UniProt
- B2UPR7
- Ligands
- NAG, MG, CL
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase, family 20, catalytic core | protein | 734 | 24% helix, 29% strand | B2UPR7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
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 | 103 | 0.58 | 0.85 | 19 | NAG |
| 2 | 122 | 0.55 | 0.83 | 26 | MG, CL |
| 3 | 180 | 0.48 | 0.76 | 28 | empty |
| 4 | 72 | 0.37 | 0.78 | 14 | empty |
| 5 | 79 | 0.35 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 6JQF · Crystallization analysis of a beta-N-acetylhexosaminidase (Am2136) from Akkermansia… · the same entry in another collection · chain A against A, TM-score 1.00
- B2UPR7 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase AMUC_2136 (B2UPR7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B2UPR7
- Elsewhere: RCSB PDB 6JQF · PDBe 6JQF · UniProt B2UPR7
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