Research workbench
Trypanosoma rangeli sialidase in complex with 2-keto-3-deoxy-D- glycero-D-galacto-2,3-difluoro-nononic acid (2,3-difluoro-kdn)
Analyse Trypanosoma rangeli sialidase in complex with 2-keto-3-deoxy-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGS
- Type
- protein
- Length
- 634 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- EC
- 3.2.1.18
- UniProt
- O44049
- Ligands
- FKD, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase (EC 3.2.1.18) | protein | 634 | 7% helix, 47% strand | O44049 |
Ligands and binding sites
- FKD · 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.58 | 0.80 | 32 | FKD |
| 2 | 214 | 0.55 | 0.78 | 23 | empty |
| 3 | 196 | 0.49 | 0.76 | 30 | SO4 |
| 4 | 80 | 0.29 | 0.72 | 20 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 2AGS · Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-glycero-D-galacto-2,3-diflu… · 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 O44049
- Elsewhere: RCSB PDB 2AGS · PDBe 2AGS · UniProt O44049
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.