Research workbench
Structure of the clostridium perfringens GH89 in complex with beta- hnjnac
Analyse Structure of the clostridium perfringens GH89 in complex with beta- hnjnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MFL
- 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
- Z8V, CA, SO4
- Pockets
- 7 · 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
- Z8V · N-[(2R,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
7 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 | 0.83 | 62 | empty |
| 2 | 269 | 0.67 | 0.83 | 26 | empty |
| 3 | 104 | 0.61 | 0.87 | 22 | EDO, Z8V |
| 4 | 183 | 0.58 | 0.81 | 33 | empty |
| 5 | 118 | 0.46 | 0.78 | 21 | empty |
Compared structures
- 7MFL · Structure of the Clostridium perfringens GH89 in complex with beta-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 7MFL · PDBe 7MFL · UniProt A0A0H2YU91
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