Research workbench
Structure of neisseria los-specific sialyltransferase (nst).
Analyse Structure of neisseria los-specific sialyltransferase (nst). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YK4
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp-N-acetylneuraminate-beta-galactosamide-alpha-2,3- sialyltransferase
- EC
- 2.4.99.-
- UniProt
- P72097
- Ligands
- EGC, SO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmp-N-acetylneuraminate-beta-galactosamide-alpha-2,3- sialyltransferase (EC 2.4.99.-) | protein | 326 | 37% helix, 21% strand | P72097 |
Ligands and binding sites
- EGC · 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-tetramethyl-butyl)-phenoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.53 | 0.75 | 36 | EDO |
| 2 | 139 | 0.45 | 0.76 | 20 | empty |
| 3 | 94 | 0.40 | 0.77 | 16 | empty |
| 4 | 61 | 0.40 | 0.80 | 15 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 2YK4 · Structure of Neisseria LOS-specific sialyltransferase (NST). · the same entry in another collection · chain A against A, TM-score 1.00
- P72097 · AlphaFold monomer V2.0 prediction for N-acetyllactosaminide alpha-2,3-sialyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.68
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 P72097
- Elsewhere: RCSB PDB 2YK4 · PDBe 2YK4 · UniProt P72097
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