MolNFT v1 · #4343 · protein
Crystal structure of class I alpha-1,2-mannosidase from saccharomyces cerevisiae at 1.54 ångström resolution
1DL2: “Crystal structure of class I alpha-1,2-mannosidase from saccharomyces cerevisiae at 1.54 ångström resolution”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.63). MolNFT v1 #4343 on GenesisL1: 3D…
- PDB
- 1DL2
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class I alpha-1,2-mannosidase
- EC
- 3.2.1.113
- UniProt
- P32906
- Ligands
- NAG, MAN, BMA, NDG, CA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class I alpha-1,2-mannosidase (EC 3.2.1.113) | protein | 510 | 50% helix, 11% strand | P32906 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 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 | 279 | 0.63 | 0.81 | 45 | CA, GOL |
| 2 | 59 | 0.47 | 0.84 | 19 | empty |
| 3 | 117 | 0.44 | 0.77 | 19 | NAG |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1DL2 · Crystal structure of class I alpha-1,2-mannosidase from saccharomyces cerevisiae at 1.54… · the same entry in another collection · chain A against A, TM-score 1.00
- P32906 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum mannosyl- oligosaccharide… · 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 P32906
- Elsewhere: RCSB PDB 1DL2 · PDBe 1DL2 · UniProt P32906
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