Research workbench
Crystal structure of the 4-fluoro rsl lectin in complex with lewis X tetrasaccharide
Analyse Crystal structure of the 4-fluoro rsl lectin in complex with lewis X… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O7W
- Type
- protein
- Length
- 178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative fucose-binding lectin protein
- UniProt
- D8NA05
- Ligands
- NAG, FUC, GAL, GLA, CA
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative fucose-binding lectin protein | protein | 89 | 0% helix, 67% strand | D8NA05 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · chains B
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · chains 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 | 51 | 0.29 | 0.75 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 228 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 modified (nonstandard).
Compared structures
- 5O7W · Crystal structure of the 4-FLUORO RSL lectin in complex with 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 5O7W · PDBe 5O7W · UniProt D8NA05
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