MolNFT v1 · #101645 · protein
Crystal structure of human alpha-galactosidase a in complex with 1- deoxygalactonojirimycin-pfpht
4NXS: “Crystal structure of human alpha-galactosidase a in complex with 1- deoxygalactonojirimycin-pfpht”. X-ray diffraction, 3 ligands (2OZ, NAG, SO4), 6 pockets (best druggability 0.56). MolNFT v1 #101645 on GenesisL1: 3D structure…
- PDB
- 4NXS
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-galactosidase a
- EC
- 3.2.1.22
- UniProt
- P06280
- Ligands
- 2OZ, NAG, SO4
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-galactosidase a (EC 3.2.1.22) | protein | 390 | 28% helix, 24% strand | P06280 |
| B | Alpha-galactosidase a (EC 3.2.1.22) | protein | 391 | 29% helix, 25% strand | P06280 |
Ligands and binding sites
- 2OZ · (2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.56 | 0.76 | 45 | empty |
| 2 | 53 | 0.40 | 0.82 | 16 | SO4 |
| 3 | 99 | 0.38 | 0.75 | 18 | empty |
| 4 | 106 | 0.37 | 0.75 | 18 | empty |
| 5 | 62 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 978 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 4NXS · PDBe 4NXS · UniProt P06280
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.