MolNFT v2 · #215031 · protein
Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)-1-methylpyrrolidine-3,4-diol
8K7K: “Crystal structure of human lysosomal alpha-galactosidase A in complex with…”. X-ray diffraction at 2, 5 ligands (VNQ, NAG, BMA), 2 pockets (best druggability 0.62). MolNFT v2 #215031 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8K7K
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Alpha-galactosidase A
- EC
- 3.2.1.22
- UniProt
- P06280
- Ligands
- VNQ, NAG, BMA, MAN, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase A (EC 3.2.1.22) | protein | 390 | 32% helix, 24% strand | P06280 |
| B | Alpha-galactosidase A (EC 3.2.1.22) | protein | 392 | 32% helix, 25% strand | P06280 |
Ligands and binding sites
- VNQ · (2~{R},3~{S},4~{R},5~{R})-2,5-bis(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.62 | 0.75 | 78 | empty |
| 2 | 62 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 994 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- P06280 · AlphaFold monomer V2.0 prediction for alpha-galactosidase a (P06280) · a predicted model of the same protein · 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 P06280
- Elsewhere: RCSB PDB 8K7K · PDBe 8K7K · UniProt P06280
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