Research workbench
Crystal structure of streptococcus pneumoniae D39 neuraminidase a precursor (nana) in complex with dana
Analyse Crystal structure of streptococcus pneumoniae D39 neuraminidase a precursor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H73
- Type
- protein
- Length
- 951 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase a
- EC
- 3.2.1.18
- UniProt
- P62576
- Ligands
- DAN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase a (EC 3.2.1.18) | protein | 474 | 6% helix, 44% strand | P62576 |
| B | Sialidase a (EC 3.2.1.18) | protein | 477 | 5% helix, 44% strand | P62576 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.76 | 0.78 | 107 | empty |
| 2 | 295 | 0.62 | 0.79 | 34 | empty |
| 3 | 277 | 0.61 | 0.79 | 26 | empty |
| 4 | 107 | 0.57 | 0.85 | 21 | DAN |
| 5 | 118 | 0.56 | 0.84 | 21 | DAN |
Interfaces
1 interface between chains.
- A–B · 1351 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3H73 · Crystal structure of Streptococcus pneumoniae D39 neuraminidase A precursor (NanA) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P62576 · AlphaFold monomer V2.0 prediction for sialidase a (P62576) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P62576
- Elsewhere: RCSB PDB 3H73 · PDBe 3H73 · UniProt P62576
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