MolNFT v1 · #182058 · protein
Structure of the clostridium perfringens GH89 in complex with alpha- hnjnac
7MFK · Alpha-N-acetylglucosaminidase family protein: “Structure of the clostridium perfringens GH89 in complex with alpha- hnjnac”. X-ray diffraction, 3 ligands (Z7S, CA, SO4), 8 pockets (best druggability 0.73). MolNFT v1 #182058 on…
- PDB
- 7MFK
- Type
- protein
- Length
- 885 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-N-acetylglucosaminidase family protein
- UniProt
- A0A0H2YU91
- Ligands
- Z7S, CA, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-N-acetylglucosaminidase family protein | protein | 885 | 41% helix, 17% strand | A0A0H2YU91 |
Ligands and binding sites
- Z7S · N-[(2S,3S,4R,5R,6R)-4,5-dihydroxy-2,6-bis(hydroxymethyl)piperidin-3-yl]acetamide · ligand · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.73 | 0.82 | 64 | empty |
| 2 | 261 | 0.66 | 0.83 | 23 | empty |
| 3 | 119 | 0.62 | 0.86 | 22 | EDO, Z7S |
| 4 | 191 | 0.58 | 0.81 | 33 | empty |
| 5 | 120 | 0.47 | 0.79 | 21 | empty |
Compared structures
- 7MFK · Structure of the Clostridium perfringens GH89 in complex with alpha-HNJNAc · 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 A0A0H2YU91
- Elsewhere: RCSB PDB 7MFK · PDBe 7MFK · UniProt A0A0H2YU91
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