MolNFT v1 · #124614 · protein
Structure of mouse golgi alpha-1,2-mannosidase ia and MAN9GLCNAC2-pa complex
5KKB · Mannosyl-oligosaccharide 1,2-alpha-mannosidase ia: “Structure of mouse golgi alpha-1,2-mannosidase ia and MAN9GLCNAC2-pa complex”. X-ray diffraction, 5 ligands (1PS, MAN, NAG), 8 pockets (best druggability 0.73). MolNFT v1 #124614…
- PDB
- 5KKB
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- 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
- 1PS, MAN, NAG, BMA, LA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-oligosaccharide 1,2-alpha-mannosidase ia (EC 3.2.1.113) | protein | 469 | 51% helix, 12% strand | P45700 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- LA · Lanthanum (III) ion · metal · 2 copies · chains A, B
- BU1 · 1,4-butanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.73 | 0.76 | 65 | empty |
| 2 | 379 | 0.65 | 0.79 | 55 | BMA, MAN, LA |
| 3 | 273 | 0.65 | 0.82 | 32 | BMA, MAN, LA |
| 4 | 147 | 0.52 | 0.80 | 19 | empty |
| 5 | 114 | 0.46 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 351 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5KKB · Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex · 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 5KKB · PDBe 5KKB · UniProt P45700
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