Research workbench
Crystal structure of the catalytic domain of clostridium perfringens neuraminidase (nani) in complex with a ches
Analyse Crystal structure of the catalytic domain of clostridium perfringens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TSP
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- UniProt
- A0A0H2YQR1
- Ligands
- CA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sialidase | protein | 448 | 3% helix, 48% strand | A0A0H2YQR1 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 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 | 1059 | 0.82 | 0.83 | 97 | NHE |
| 2 | 330 | 0.63 | 0.79 | 37 | empty |
| 3 | 245 | 0.61 | 0.80 | 25 | empty |
| 4 | 299 | 0.61 | 0.79 | 33 | empty |
| 5 | 141 | 0.51 | 0.80 | 21 | NHE |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5TSP · Crystal structure of the catalytic domain of Clostridium perfringens neuraminidase (NanI)… · 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 A0A0H2YQR1
- Elsewhere: RCSB PDB 5TSP · PDBe 5TSP · UniProt A0A0H2YQR1
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