Research workbench
Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate
Analyse Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AP6
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-8
- UniProt
- O00214
- Ligands
- BGC, GAL, SO4
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-8 | protein | 146 | 2% helix, 55% strand | O00214 |
| B | Galectin-8 | protein | 145 | 2% helix, 52% strand | O00214 |
| C | Galectin-8 | protein | 145 | 2% helix, 56% strand | O00214 |
| D | Galectin-8 | protein | 147 | 2% helix, 55% strand | O00214 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.59 | 0.76 | 60 | empty |
| 2 | 256 | 0.53 | 0.76 | 29 | empty |
| 3 | 161 | 0.44 | 0.75 | 25 | empty |
| 4 | 60 | 0.43 | 0.82 | 15 | empty |
| 5 | 83 | 0.36 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 476 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 420 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 64 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3AP6 · Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- O00214 · AlphaFold monomer V2.0 prediction for galectin-8 (O00214) · a predicted model of the same protein · chain C 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 O00214
- Elsewhere: RCSB PDB 3AP6 · PDBe 3AP6 · UniProt O00214
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.