Research workbench
Crystal structure of calsepa lectin in complex with biantennary N- glycan
Analyse Crystal structure of calsepa lectin in complex with biantennary N- glycan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XFI
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- P93114
- Ligands
- BEZ, NAG, MAN, BMA, GAL, SO4
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 152 | 0% helix, 63% strand | P93114 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies
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 | 61 | 0.29 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1265 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5XFI · Crystal structure of Calsepa lectin in complex with biantennary N-glycan · the same entry in another collection · chain A against A, TM-score 1.00
- P93114 · AlphaFold monomer V2.0 prediction for jacalin-related lectin calsepa (P93114) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P93114
- Elsewhere: RCSB PDB 5XFI · PDBe 5XFI · UniProt P93114
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