MolNFT v1 · #128655 · protein
Mouse galactocerebrosidase in complex with saposin a
5NXB: “Mouse galactocerebrosidase in complex with saposin a”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 12 pockets (best druggability 0.86). MolNFT v1 #128655 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NXB
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactocerebrosidase; Prosaposin
- EC
- 3.2.1.46
- UniProt
- P54818, Q61207
- Ligands
- NAG, BMA, CA
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galactocerebrosidase (EC 3.2.1.46) | protein | 644 | 18% helix, 35% strand | P54818 |
| C, D | Prosaposin | protein | 80 | 79% helix, 1% strand | Q61207 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.86 | 0.86 | 94 | empty |
| 2 | 402 | 0.67 | 0.80 | 49 | empty |
| 3 | 368 | 0.65 | 0.79 | 45 | empty |
| 4 | 111 | 0.56 | 0.83 | 19 | empty |
| 5 | 269 | 0.56 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1028 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1013 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 434 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5NXB · Mouse galactocerebrosidase in complex with saposin A · 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
- Q61207 · AlphaFold monomer V2.0 prediction for prosaposin (Q61207) · a predicted model of the same protein · chain C against A, TM-score 0.58
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
- Every structure of UniProt Q61207
- Elsewhere: RCSB PDB 5NXB · PDBe 5NXB · UniProt P54818 · UniProt Q61207
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