Research workbench
X-ray structure of rsl lectin in complex with sialyl lewis X tetrasaccharide
Analyse X-ray structure of rsl lectin in complex with sialyl lewis X tetrasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AJC
- Type
- protein
- Length
- 267 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative fucose-binding lectin protein
- UniProt
- D8NA05
- Ligands
- FUC, FUL, NDG, GAL, NAG, SIA
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 70% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative fucose-binding lectin protein | protein | 89 | 0% helix, 70% strand | D8NA05 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B, C
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.74 | 0.80 | 75 | empty |
Interfaces
3 interfaces between chains.
- B–C · 798 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 730 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5AJC · X-ray structure of RSL lectin in complex with sialyl lewis X tetrasaccharide · 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 D8NA05
- Elsewhere: RCSB PDB 5AJC · PDBe 5AJC · UniProt D8NA05
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