Research workbench
Structure of human sialyltransferase ST8SIAIII in complex with CTP
Analyse Structure of human sialyltransferase ST8SIAIII in complex with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BO7
- Type
- protein
- Length
- 569 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
- CTP, NAG, FUC
- Pockets
- 8 · best druggability 0.70
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 | 290 | 39% helix, 13% strand | O43173 |
| B | Sia-alpha-2,3-gal-beta-1,4-glcnac-R:ALPHA 2,8- sialyltransferase (EC 2.4.99.-) | protein | 279 | 41% helix, 14% strand | O43173 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.70 | 0.80 | 52 | CTP |
| 2 | 381 | 0.69 | 0.81 | 45 | CTP |
| 3 | 50 | 0.55 | 0.90 | 18 | empty |
| 4 | 161 | 0.51 | 0.78 | 21 | empty |
| 5 | 86 | 0.40 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5BO7 · Structure of human sialyltransferase ST8SiaIII in complex with CTP · 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 A against A, TM-score 0.99
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 5BO7 · PDBe 5BO7 · UniProt O43173
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