Research workbench
Ttgala, alpha-galactosidase from thermus thermophilus in complex with stachyose
Analyse Ttgala, alpha-galactosidase from thermus thermophilus in complex with stachyose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCL
- Type
- protein
- Length
- 1,413 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- UniProt
- Q53W51
- Ligands
- GLA
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Alpha-galactosidase | protein | 479 | 30% helix, 29% strand | Q53W51 |
| C | Alpha-galactosidase | protein | 455 | 31% helix, 28% strand | Q53W51 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.72 | 0.78 | 72 | empty |
| 2 | 175 | 0.62 | 0.84 | 27 | GLA |
| 3 | 191 | 0.61 | 0.82 | 28 | GLA |
| 4 | 183 | 0.59 | 0.81 | 28 | GLA |
| 5 | 230 | 0.56 | 0.78 | 36 | empty |
Interfaces
2 interfaces between chains.
- C–E · 761 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LCL · TtGalA, alpha-galactosidase from Thermus thermophilus in complex with stachyose · the same entry in another collection · chain A 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 Q53W51
- Elsewhere: RCSB PDB 6LCL · PDBe 6LCL · UniProt Q53W51
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