Research workbench
Mouse galactocerebrosidase complexed with galacto-noeurostegine gns at pH 6.8
Analyse Mouse galactocerebrosidase complexed with galacto-noeurostegine gns at pH 6.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y6S
- Type
- protein
- Length
- 641 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
- ODW, NAG, CA, NI
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactocerebrosidase (EC 3.2.1.46) | protein | 641 | 18% helix, 35% strand | P54818 |
Ligands and binding sites
- ODW · (1~{R},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-1,2,3-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- CA · Calcium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.47 | 0.83 | 18 | empty |
| 2 | 64 | 0.46 | 0.83 | 14 | ODW |
| 3 | 114 | 0.36 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 4 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6Y6S · Mouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 6.8 · 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 6Y6S · PDBe 6Y6S · UniProt P54818
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