Research workbench
Ttgala, alpha-galactosidase from thermus thermophilus in complex with P-nitrophenyl alpha-D-galactopyranoside (alpha-npg)
Analyse Ttgala, alpha-galactosidase from thermus thermophilus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCK
- Type
- protein
- Length
- 1,437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- UniProt
- Q53W51
- Ligands
- 9PG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-galactosidase | protein | 479 | 30% helix, 31% strand | Q53W51 |
Ligands and binding sites
- 9PG · 4-nitrophenyl alpha-D-galactopyranoside · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.82 | 0.83 | 92 | 9PG |
| 2 | 186 | 0.63 | 0.83 | 30 | 9PG |
| 3 | 245 | 0.58 | 0.79 | 34 | empty |
| 4 | 259 | 0.57 | 0.78 | 36 | empty |
| 5 | 131 | 0.55 | 0.82 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 905 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6LCK · TtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl… · 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 6LCK · PDBe 6LCK · UniProt Q53W51
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