Research workbench
Crystal structure of galectin 8 with NDP52 peptide
Analyse Crystal structure of galectin 8 with NDP52 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAN
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-8; Calcium-binding and coiled-coil domain-containing protein 2
- UniProt
- O00214, Q13137
- Ligands
- NAD
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galectin-8 | protein | 293 | 2% helix, 57% strand | O00214 |
| C, D | Calcium-binding and coiled-coil domain-containing protein 2 | protein | 9 | 0% helix, 0% strand | Q13137 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.77 | 0.79 | 82 | empty |
| 2 | 91 | 0.41 | 0.78 | 19 | empty |
| 3 | 86 | 0.37 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1661 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 536 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4HAN · Crystal structure of Galectin 8 with NDP52 peptide · 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 A against A, TM-score 0.59
- Q13137 · AlphaFold monomer V2.0 prediction for calcium-binding and coiled-coil domain-containing… · a predicted model of the same protein · chain D against A, TM-score 0.33
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
- Every structure of UniProt Q13137
- Elsewhere: RCSB PDB 4HAN · PDBe 4HAN · UniProt O00214 · UniProt Q13137
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