MolNFT v1 · #184763 · protein
Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole D-galactal ligand
7P1M: “Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole D-galactal ligand”. X-ray diffraction, 2 ligands (4IU, CL), 2 pockets (best druggability 0.47). MolNFT v1 #184763 on GenesisL1: 3D structure…
- PDB
- 7P1M
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-8
- UniProt
- O00214
- Ligands
- 4IU, CL
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-8 | protein | 150 | 2% helix, 54% strand | O00214 |
| B | Galectin-8 | protein | 149 | 2% helix, 53% strand | O00214 |
Ligands and binding sites
- 4IU · 2-[[(2R,3R,4R)-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2H-pyran-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.47 | 0.76 | 26 | empty |
| 2 | 58 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7P1M · Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole… · the same entry in another collection · chain A against A, TM-score 1.00
- O00214 · AlphaFold monomer V2.0 prediction for galectin-8 (O00214) · a predicted model of the same protein · chain B 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 O00214
- Elsewhere: RCSB PDB 7P1M · PDBe 7P1M · UniProt O00214
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