MolNFT v1 · #110102 · protein
Crystal structure of the K499G mutant of nanb sialidase from streptococcus pneumoniae
4XMI · Sialidase B: “Crystal structure of the K499G mutant of nanb sialidase from streptococcus pneumoniae”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.62). MolNFT v1 #110102 on GenesisL1: 3D structure, binding sites…
- 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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