MolNFT v1 · #50438 · protein
Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog
2RI9 · Mannosyl-oligosaccharide alpha-1,2-mannosidase: “Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog”. X-ray diffraction, 6 ligands (LDY, NAG, MAN), 4 pockets (best druggability 0.79). MolNFT v1 #50438 on…
- PDB
- 2RI9
- 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
- LDY, NAG, MAN, NDG, MMA, CA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannosyl-oligosaccharide alpha-1,2-mannosidase (EC 3.2.1.113) | protein | 475 | 51% helix, 11% strand | P31723 |
Ligands and binding sites
- LDY · alpha-D-lyxopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- MMA · methyl alpha-D-mannopyranoside · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 669 | 0.79 | 0.84 | 86 | empty |
| 2 | 344 | 0.66 | 0.81 | 46 | MMA, LDY, CA, GOL |
| 3 | 103 | 0.61 | 0.87 | 20 | MMA, LDY, CA, GOL |
| 4 | 69 | 0.34 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 2RI9 · Penicillium citrinum alpha-1,2-mannosidase in complex with a substrate analog · 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 2RI9 · PDBe 2RI9 · UniProt P31723
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