MolNFT v1 · #60884 · protein
Golgi mannosidase II complex with an N-aryl carbamate derivative of gluco-hydroxyiminolactam
3D52 · Alpha-mannosidase 2: “Golgi mannosidase II complex with an N-aryl carbamate derivative of gluco-hydroxyiminolactam”. X-ray diffraction, 2 ligands (GHR, ZN), 11 pockets (best druggability 0.81). MolNFT v1 #60884 on GenesisL1: 3D…
- PDB
- 3D52
- Type
- protein
- Length
- 1,016 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
- GHR, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-mannosidase 2 (EC 3.2.1.114) | protein | 1016 | 24% helix, 31% strand | Q24451 |
Ligands and binding sites
- GHR · [[(3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-ylidene]amino] N-(4-chlorophenyl)carbamate · ligand · chains A
- ZN · Zinc ion · metal · 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.81 | 0.98 | 32 | empty |
| 2 | 872 | 0.80 | 0.82 | 125 | empty |
| 3 | 236 | 0.62 | 0.81 | 32 | empty |
| 4 | 250 | 0.54 | 0.77 | 37 | GHR |
| 5 | 140 | 0.51 | 0.80 | 18 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3D52 · GOLGI MANNOSIDASE II complex with an N-aryl carbamate derivative of… · 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 3D52 · PDBe 3D52 · UniProt Q24451
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