Research workbench
Crystal structure of the glycoside hydrolase family 36 alpha- galactosidase from paecilomyces thermophila
Analyse Crystal structure of the glycoside hydrolase family 36 alpha- galactosidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JHP
- Type
- protein
- Length
- 2,864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- A0A2Z4HIN9
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-galactosidase (EC 3.2.1.22) | protein | 716 | 21% helix, 32% strand | A0A2Z4HIN9 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.89 | 0.94 | 109 | empty |
| 2 | 722 | 0.87 | 0.91 | 112 | empty |
| 3 | 596 | 0.77 | 0.84 | 51 | empty |
| 4 | 648 | 0.76 | 0.82 | 50 | empty |
| 5 | 698 | 0.76 | 0.81 | 99 | TRS |
Interfaces
6 interfaces between chains.
- A–D · 2903 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2870 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2015 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1995 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6JHP · Crystal structure of the glycoside hydrolase family 36 alpha-galactosidase from… · 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 A0A2Z4HIN9
- Elsewhere: RCSB PDB 6JHP · PDBe 6JHP · UniProt A0A2Z4HIN9
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