Research workbench
Crystal structure of the nanb sialidase from streptococcus pneumoniae in complex with 5-acetamido-2,3-difluoro-3-hydroxy-6-[1,2,3- TRIHYDROXYPROPYL]OXANE-2-carboxylic acid
Analyse Crystal structure of the nanb sialidase from streptococcus pneumoniae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJA
- 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
- OPX, SFJ, PO4
- Pockets
- 5 · best druggability 0.62
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
- OPX · (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid · ligand · chains A
- SFJ · (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.62 | 0.79 | 26 | OPX |
| 2 | 322 | 0.62 | 0.79 | 36 | SFJ |
| 3 | 293 | 0.55 | 0.76 | 32 | empty |
| 4 | 204 | 0.51 | 0.76 | 33 | DMS |
| 5 | 71 | 0.41 | 0.79 | 14 | empty |
Compared structures
- 4XJA · Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with… · 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 4XJA · PDBe 4XJA · UniProt Q54727
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