MolNFT v1 · #124559 · protein
Srpa with sialyl lewisx
5KIQ · Platelet-binding glycoprotein: “Srpa with sialyl lewisx”. X-ray diffraction, 5 ligands (NAG, GAL, SIA), 1 pocket (best druggability 0.27). MolNFT v1 #124559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KIQ
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-binding glycoprotein
- UniProt
- A3CM52
- Ligands
- NAG, GAL, SIA, FUC, CA
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-binding glycoprotein | protein | 197 | 12% helix, 36% strand | A3CM52 |
| B | Platelet-binding glycoprotein | protein | 193 | 12% helix, 36% strand | A3CM52 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 7 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.27 | 0.74 | 17 | ACT |
Interfaces
1 interface between chains.
- A–B · 568 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5KIQ · SrpA with sialyl LewisX · 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 A3CM52
- Elsewhere: RCSB PDB 5KIQ · PDBe 5KIQ · UniProt A3CM52
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