Research workbench
Structure of alpha-galactosidase from lactobacillus acidophilus ncfm with tris
Analyse Structure of alpha-galactosidase from lactobacillus acidophilus ncfm with tris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XN1
- Type
- protein
- Length
- 2,916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase
- EC
- 3.2.1.22
- UniProt
- Q7WWP9
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-galactosidase (EC 3.2.1.22) | protein | 729 | 22% helix, 32% strand | Q7WWP9 |
Ligands and binding sites
- GOL · Glycerol · additive · 21 copies · chains A, B, D, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.87 | 0.90 | 92 | empty |
| 2 | 774 | 0.86 | 0.90 | 90 | empty |
| 3 | 1033 | 0.82 | 0.83 | 125 | empty |
| 4 | 365 | 0.75 | 0.86 | 66 | TRS, GOL |
| 5 | 587 | 0.74 | 0.81 | 60 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3228 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3222 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 2348 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2342 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 960 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2XN1 · Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with TRIS · 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 Q7WWP9
- Elsewhere: RCSB PDB 2XN1 · PDBe 2XN1 · UniProt Q7WWP9
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