Research workbench
Two copies of the catalytic domain of nana sialidase from streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with dana
Analyse Two copies of the catalytic domain of nana sialidase from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A54
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase a
- EC
- 3.2.1.18
- UniProt
- P62575
- Ligands
- DAN
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sialidase a (EC 3.2.1.18) | protein | 472 | 6% helix, 46% strand | P62575 |
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
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.72 | 0.79 | 63 | empty |
| 2 | 321 | 0.63 | 0.79 | 37 | empty |
| 3 | 299 | 0.59 | 0.78 | 26 | empty |
| 4 | 140 | 0.57 | 0.82 | 21 | DAN |
| 5 | 157 | 0.57 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1275 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7A54 · Two copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae… · the same entry in another collection · chain A against A, TM-score 1.00
- P62575 · AlphaFold monomer V2.0 prediction for sialidase a (P62575) · 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 P62575
- Elsewhere: RCSB PDB 7A54 · PDBe 7A54 · UniProt P62575
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