Research workbench
Crystal structure of the gspb siglec domain with sialyl T antigen bound
Analyse Crystal structure of the gspb siglec domain with sialyl T antigen bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IUC
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet binding protein gspb
- UniProt
- Q939N5
- Ligands
- A2G, GAL, SIA, MG
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Platelet binding protein gspb | protein | 123 | 10% helix, 43% strand | Q939N5 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.71 | 0.78 | 71 | GAL |
| 2 | 121 | 0.52 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 455 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5IUC · Crystal structure of the GspB siglec domain with sialyl T antigen bound · the same entry in another collection · 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 Q939N5
- Elsewhere: RCSB PDB 5IUC · PDBe 5IUC · UniProt Q939N5
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