MolNFT v1 · #107615 · protein
Mouse galactocerebrosidase complexed with 1-deoxy-galacto-nojirimycin dgj
4UFM: “Mouse galactocerebrosidase complexed with 1-deoxy-galacto-nojirimycin dgj”. X-ray diffraction, 3 ligands (DGJ, NAG, CA), 4 pockets (best druggability 0.48). MolNFT v1 #107615 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4UFM
- Type
- protein
- Length
- 640 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactocerebrosidase
- EC
- 3.2.1.46
- UniProt
- P54818
- Ligands
- DGJ, NAG, CA
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactocerebrosidase (EC 3.2.1.46) | protein | 640 | 18% helix, 34% strand | P54818 |
Ligands and binding sites
- DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.48 | 0.84 | 17 | empty |
| 2 | 67 | 0.45 | 0.82 | 14 | DGJ |
| 3 | 99 | 0.36 | 0.74 | 18 | empty |
| 4 | 52 | 0.25 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 4UFM · Mouse Galactocerebrosidase complexed with 1-deoxy-galacto-nojirimycin DGJ · the same entry in another collection · chain A against A, TM-score 1.00
- P54818 · AlphaFold monomer V2.0 prediction for galactocerebrosidase (P54818) · 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 P54818
- Elsewhere: RCSB PDB 4UFM · PDBe 4UFM · UniProt P54818
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