MolNFT v1 · #122233 · protein
Srpa adhesin in complex with sialyllactosamine
5IJ2 · Platelet-binding glycoprotein: “Srpa adhesin in complex with sialyllactosamine”. X-ray diffraction, 4 ligands (NAG, GAL, SIA), 1 pocket (best druggability 0.25). MolNFT v1 #122233 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IJ2
- Type
- protein
- Length
- 394 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, CA
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-binding glycoprotein | protein | 201 | 13% helix, 35% 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
- CA · Calcium ion · metal · 7 copies · chains A, B
- ACT · Acetate ion · additive · 5 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 | 0.25 | 0.73 | 18 | ACT |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5IJ2 · SrpA adhesin in complex with sialyllactosamine · 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 5IJ2 · PDBe 5IJ2 · UniProt A3CM52
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.