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Structure of P. citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the er and golgi class I enzymes
Analyse Structure of P. citrinum alpha 1,2-mannosidase reveals the basis for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KRF
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-oligosaccharide alpha-1,2-mannosidase
- EC
- 3.2.1.113
- UniProt
- P31723
- Ligands
- KIF, NAG, MAN, CA
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-oligosaccharide alpha-1,2-mannosidase (EC 3.2.1.113) | protein | 475 | 52% helix, 12% strand | P31723 |
Ligands and binding sites
- KIF · Kifunensine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.77 | 0.84 | 76 | empty |
| 2 | 122 | 0.60 | 0.86 | 21 | CA, KIF |
| 3 | 90 | 0.57 | 0.87 | 19 | CA, KIF |
| 4 | 75 | 0.45 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 1KRF · Structure of P. citrinum alpha 1,2-mannosidase reveals the basis for differences in… · the same entry in another collection · chain A against A, TM-score 1.00
- P31723 · AlphaFold monomer V2.0 prediction for mannosyl-oligosaccharide alpha-1,2-mannosidase… · 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 P31723
- Elsewhere: RCSB PDB 1KRF · PDBe 1KRF · UniProt P31723
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