Research workbench
Structure of the catalytic domain of the native nana sialidase from streptococcus pneumoniae
Analyse Structure of the catalytic domain of the native nana sialidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W20
- Type
- protein
- Length
- 939 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
- CL
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase a (EC 3.2.1.18) | protein | 470 | 6% helix, 45% strand | P62576 |
| B | Sialidase a (EC 3.2.1.18) | protein | 469 | 6% helix, 45% strand | P62576 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.74 | 0.77 | 102 | empty |
| 2 | 287 | 0.62 | 0.80 | 29 | empty |
| 3 | 315 | 0.60 | 0.78 | 27 | empty |
| 4 | 154 | 0.55 | 0.81 | 22 | empty |
| 5 | 153 | 0.52 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1202 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2W20 · Structure of the catalytic domain of the native NanA sialidase from Streptococcus… · 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 B 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 2W20 · PDBe 2W20 · UniProt P62576
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