MolNFT v1 · #41339 · protein
Crystal structure of streptococcus pneumoniae nanb in complex with 2,7-anhydro-NEU5AC
2JKB · Sialidase B: “Crystal structure of streptococcus pneumoniae nanb in complex with 2,7-anhydro-NEU5AC”. X-ray diffraction, 1 ligand (SKD), 5 pockets (best druggability 0.63). MolNFT v1 #41339 on GenesisL1: 3D structure, binding sites…
- PDB
- 2JKB
- Type
- protein
- Length
- 661 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase B
- EC
- 4.2.2.15
- UniProt
- Q54727
- Ligands
- SKD
- Pockets
- 5 · 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 4.2.2.15) | protein | 661 | 3% helix, 45% strand | Q54727 |
Ligands and binding sites
- SKD · 2-acetylamino-7-(1,2-dihydroxy-ethyl)-3-hydroxy-6,8-dioxa-bicyclo[3.2.1]octane-5-carboxylic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.63 | 0.80 | 30 | EDO |
| 2 | 253 | 0.60 | 0.80 | 37 | SKD |
| 3 | 195 | 0.52 | 0.77 | 31 | EDO |
| 4 | 158 | 0.45 | 0.76 | 23 | empty |
| 5 | 81 | 0.41 | 0.78 | 15 | empty |
Compared structures
- 2JKB · Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac · 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 2JKB · PDBe 2JKB · UniProt Q54727
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