Research workbench
Structure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal solubilizing antibody, 6F5
Analyse Structure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKU
- Type
- protein
- Length
- 568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.91
- Source
- Homo sapiens; Lama glama
- Molecule
- Galectin-10; Fab 6F5 - Heavy Chain; Fab 6F5 - Light chain
- UniProt
- Q05315
- Ligands
- CA
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.91 · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-10 | protein | 140 | 4% helix, 56% strand | Q05315 |
| H | Fab 6F5 - Heavy Chain | protein | 214 | 8% helix, 52% strand | — |
| L | Fab 6F5 - Light chain | protein | 214 | 7% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.58 | 0.74 | 58 | PGE |
| 2 | 157 | 0.48 | 0.77 | 27 | empty |
| 3 | 160 | 0.46 | 0.76 | 30 | empty |
| 4 | 138 | 0.43 | 0.76 | 26 | empty |
| 5 | 62 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1837 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 586 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 285 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GKU · Structure of galectin-10 in complex with the Fab fragment of a charcot-leyden crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05315 · AlphaFold monomer V2.0 prediction for galectin-10 (Q05315) · 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 Q05315
- Elsewhere: RCSB PDB 6GKU · PDBe 6GKU · UniProt Q05315
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