MolNFT v1 · #150138 · protein
X-ray structure of a non-autocrystallizing galectin-10 variant, GAL10- TYR69GLU
6GKT: “X-ray structure of a non-autocrystallizing galectin-10 variant, GAL10- TYR69GLU”. X-ray diffraction, 10 pockets (best druggability 0.75). MolNFT v1 #150138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GKT
- Type
- protein
- Length
- 836 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-10
- UniProt
- Q05315
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Galectin-10 | protein | 140 | 4% helix, 56% strand | Q05315 |
| B | Galectin-10 | protein | 141 | 4% helix, 55% strand | Q05315 |
| C | Galectin-10 | protein | 138 | 4% helix, 54% strand | Q05315 |
| F | Galectin-10 | protein | 137 | 4% helix, 55% strand | Q05315 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 8 copies · chains A, B, C, E, F
- PG4 · Tetraethylene glycol · additive · chains A, B
- P6G · Hexaethylene glycol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.75 | 0.78 | 78 | empty |
| 2 | 358 | 0.62 | 0.78 | 48 | PGE |
| 3 | 253 | 0.58 | 0.79 | 33 | PGE |
| 4 | 259 | 0.54 | 0.77 | 39 | empty |
| 5 | 236 | 0.54 | 0.77 | 38 | empty |
Interfaces
7 interfaces between chains.
- C–D · 876 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 864 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 521 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 312 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GKT · X-ray structure of a non-autocrystallizing galectin-10 variant, Gal10-Tyr69Glu · the same entry in another collection · chain F against F, TM-score 1.00
- Q05315 · AlphaFold monomer V2.0 prediction for galectin-10 (Q05315) · a predicted model of the same protein · chain F 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 Q05315
- Elsewhere: RCSB PDB 6GKT · PDBe 6GKT · UniProt Q05315
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