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X-ray crystallography reveals crosslinking of mammalian lectin (galectin-1) by biantennary complex type saccharides
Analyse X-ray crystallography reveals crosslinking of mammalian lectin (galectin-1) by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SLC
- Type
- protein
- Length
- 535 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bovine galectin-1
- UniProt
- P11116
- Ligands
- NAG, MAN, GAL, BMA, NDG
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Bovine galectin-1 | protein | 134 | 2% helix, 64% strand | P11116 |
| C | Bovine galectin-1 | protein | 133 | 0% helix, 65% strand | P11116 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.52 | 0.76 | 28 | empty |
| 2 | 151 | 0.48 | 0.77 | 19 | empty |
| 3 | 74 | 0.42 | 0.80 | 17 | empty |
| 4 | 103 | 0.40 | 0.76 | 15 | empty |
| 5 | 59 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 562 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1SLC · X-ray crystallography reveals crosslinking of mammalian lectin (galectin-1) by… · the same entry in another collection · chain A against A, TM-score 1.00
- P11116 · AlphaFold monomer V2.0 prediction for galectin-1 (P11116) · a predicted model of the same protein · chain C 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 P11116
- Elsewhere: RCSB PDB 1SLC · PDBe 1SLC · UniProt P11116
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