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Structure of mouse golgi alpha-1,2-mannosidase ia reveals the molecular basis for substrate specificity among class I enzymes (family 47 glycosidases)
Analyse Structure of mouse golgi alpha-1,2-mannosidase ia reveals the molecular basis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NXC
- Type
- protein
- Length
- 467 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-oligosaccharide 1,2-alpha-mannosidase ia
- EC
- 3.2.1.113
- UniProt
- P45700
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-oligosaccharide 1,2-alpha-mannosidase ia (EC 3.2.1.113) | protein | 467 | 50% helix, 12% strand | P45700 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.66 | 0.79 | 57 | CA |
| 2 | 93 | 0.40 | 0.77 | 16 | empty |
| 3 | 93 | 0.38 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1NXC · Structure of mouse Golgi alpha-1,2-mannosidase IA reveals the molecular basis for… · the same entry in another collection · chain A against A, TM-score 1.00
- P45700 · AlphaFold monomer V2.0 prediction for mannosyl-oligosaccharide 1,2-alpha-mannosidase ia… · 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 P45700
- Elsewhere: RCSB PDB 1NXC · PDBe 1NXC · UniProt P45700
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