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Structure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal solubilizing antibody, 1D11
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
- 6GLW
- Type
- protein
- Length
- 1,155 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens; Lama glama
- Molecule
- Galectin-10; Fab 1D11 - Heavy chain; Fab 1D11 - Light chain
- UniProt
- Q05315
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.9 · 6 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-10 | protein | 139 | 4% helix, 54% strand | Q05315 |
| B | Galectin-10 | protein | 139 | 4% helix, 54% strand | Q05315 |
| C | Fab 1D11 - Heavy chain | protein | 218 | 8% helix, 50% strand | — |
| D | Fab 1D11 - Light chain | protein | 213 | 8% helix, 51% strand | — |
| H | Fab 1D11 - Heavy chain | protein | 230 | 8% helix, 48% strand | — |
| L | Fab 1D11 - Light chain | protein | 216 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.61 | 0.81 | 25 | empty |
| 2 | 514 | 0.58 | 0.73 | 52 | empty |
| 3 | 241 | 0.58 | 0.79 | 27 | empty |
| 4 | 235 | 0.55 | 0.77 | 33 | empty |
| 5 | 335 | 0.52 | 0.73 | 40 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1916 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 908 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 508 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6GLW · Structure of galectin-10 in complex with the Fab fragment of a charcot-leyden crystal… · the same entry in another collection · chain L against L, 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 0.98
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 6GLW · PDBe 6GLW · UniProt Q05315
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