Research workbench
Structure of neisseria los-specific sialyltransferase (nst), in complex with cmp.
Analyse Structure of neisseria los-specific sialyltransferase (nst), in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YK5
- 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
- C, SO4, PO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% 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 | 35% helix, 20% strand | P72097 |
Ligands and binding sites
- C · Cytidine-5'-monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.62 | 0.77 | 48 | C, EDO |
| 2 | 168 | 0.47 | 0.76 | 22 | empty |
| 3 | 90 | 0.46 | 0.80 | 17 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 2YK5 · Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP. · 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 0.67
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 2YK5 · PDBe 2YK5 · UniProt P72097
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