Research workbench
Crystal structure of apo nanb sialidase from streptococcus pneumoniae at pH 7.4 in pbs with dmso
Analyse Crystal structure of apo nanb sialidase from streptococcus pneumoniae at pH 7.4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJZ
- Type
- protein
- Length
- 658 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase B
- EC
- 3.2.1.18
- UniProt
- Q54727
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase B (EC 3.2.1.18) | protein | 658 | 3% helix, 45% strand | Q54727 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.63 | 0.78 | 39 | DMS |
| 2 | 344 | 0.62 | 0.79 | 28 | DMS |
| 3 | 196 | 0.50 | 0.76 | 32 | DMS |
| 4 | 208 | 0.48 | 0.75 | 23 | empty |
| 5 | 77 | 0.40 | 0.79 | 16 | empty |
Compared structures
- 4XJZ · Crystal structure of apo NanB sialidase from streptococcus pneumoniae at pH 7.4 in PBS… · the same entry in another collection · chain A against A, TM-score 1.00
- Q54727 · AlphaFold monomer V2.0 prediction for sialidase B (Q54727) · 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 Q54727
- Elsewhere: RCSB PDB 4XJZ · PDBe 4XJZ · UniProt Q54727
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