MolNFT v1 · #52478 · protein
Structure of the catalytic domain of the native nana sialidase from streptococcus pneumoniae
2W20 · Sialidase a: “Structure of the catalytic domain of the native nana sialidase from streptococcus pneumoniae”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.74). MolNFT v1 #52478 on GenesisL1: 3D structure, binding…
- 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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