Research workbench
The structures of salmonella typhimurium LT2 neuraminidase and its complex with a transition state analogue at 1.6 ångströms resolution
Analyse The structures of salmonella typhimurium LT2 neuraminidase and its complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2SIM
- Type
- protein
- Length
- 381 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- EC
- 3.2.1.18
- UniProt
- P29768
- Ligands
- DAN
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase (EC 3.2.1.18) | protein | 381 | 6% helix, 47% strand | P29768 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.66 | 0.81 | 29 | empty |
| 2 | 199 | 0.54 | 0.79 | 32 | DAN |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2SIM · The structures of salmonella typhimurium LT2 neuraminidase and its complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P29768 · AlphaFold monomer V2.0 prediction for sialidase (P29768) · a predicted model of the same protein · 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 P29768
- Elsewhere: RCSB PDB 2SIM · PDBe 2SIM · UniProt P29768
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