MolNFT v1 · #114395 · protein
Structure of human sialyltransferase ST8SIAIII in complex with cdp
5BO6 · Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8…: “Structure of human sialyltransferase ST8SIAIII in complex with cdp”. X-ray diffraction, 4 ligands (CDP, NAG, BMA), 6 pockets (best druggability 0.76). MolNFT v1 #114395 on GenesisL1…
- PDB
- 5BO6
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase
- EC
- 2.4.99.-
- UniProt
- O43173
- Ligands
- CDP, NAG, BMA, FUC
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase (EC 2.4.99.-) | protein | 291 | 38% helix, 13% strand | O43173 |
| B | Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase (EC 2.4.99.-) | protein | 277 | 41% helix, 14% strand | O43173 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.76 | 0.86 | 44 | CDP |
| 2 | 332 | 0.62 | 0.79 | 45 | CDP |
| 3 | 137 | 0.47 | 0.78 | 18 | empty |
| 4 | 129 | 0.43 | 0.76 | 18 | empty |
| 5 | 88 | 0.41 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1036 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5BO6 · Structure of human sialyltransferase ST8SiaIII in complex with CDP · the same entry in another collection · chain A against A, TM-score 1.00
- O43173 · AlphaFold monomer V2.0 prediction for sia-alpha-2,3-gal- beta-1,4-glcnac-R:ALPHA… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O43173
- Elsewhere: RCSB PDB 5BO6 · PDBe 5BO6 · UniProt O43173
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