MolNFT v1 · #61165 · protein
Golgi mannosidase II complex with (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)- 2-hydroxy-1 PHENYLETHYL]AMINO}METHYL) methylpyrrolidin-2-one
3DDG · Alpha-mannosidase 2: “Golgi mannosidase II complex with (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)- 2-hydroxy-1 PHENYLETHYL]AMINO}METHYL)…”. X-ray diffraction, 4 ligands (GB7, NAG, ZN), 12 pockets (best druggability 0.80). MolNFT v1 #61165…
- PDB
- 3DDG
- Type
- protein
- Length
- 1,015 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-mannosidase 2
- EC
- 3.2.1.114
- UniProt
- Q24451
- Ligands
- GB7, NAG, ZN, PO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase 2 (EC 3.2.1.114) | protein | 1015 | 24% helix, 30% strand | Q24451 |
Ligands and binding sites
- GB7 · (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-1-methylpyrrolidin-2-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.80 | 0.97 | 30 | empty |
| 2 | 330 | 0.75 | 0.87 | 51 | empty |
| 3 | 608 | 0.73 | 0.80 | 92 | PO4 |
| 4 | 276 | 0.65 | 0.82 | 29 | empty |
| 5 | 227 | 0.52 | 0.76 | 32 | GB7 |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3DDG · GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1… · the same entry in another collection · 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 Q24451
- Elsewhere: RCSB PDB 3DDG · PDBe 3DDG · UniProt Q24451
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