Research workbench
Crystal structure of the K499G mutant of nanb sialidase from streptococcus pneumoniae
Analyse Crystal structure of the K499G mutant of nanb 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
- 4XMI
- 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
- 7 · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.62 | 0.79 | 41 | PO4 |
| 2 | 296 | 0.58 | 0.78 | 29 | DMS |
| 3 | 236 | 0.54 | 0.77 | 34 | DMS |
| 4 | 267 | 0.54 | 0.75 | 33 | empty |
| 5 | 74 | 0.39 | 0.78 | 16 | DMS |
Compared structures
- 4XMI · Crystal structure of the K499G mutant of NanB sialidase from Streptococcus pneumoniae · 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 4XMI · PDBe 4XMI · UniProt Q54727
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