MolNFT v1 · #61164 · protein
Golgi mannosidase II complex with (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)- 2-hydroxy-1 PHENYLETHYL]AMINO}METHYL) pyrrolidin-2-one
3DDF · 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, 3 ligands (GB6, NAG, ZN), 13 pockets (best druggability 0.80). MolNFT v1 #61164…
- PDB
- 3DDF
- 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
- GB6, NAG, ZN
- Pockets
- 13 · 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
- GB6 · (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidin-2-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 30 | empty |
| 2 | 322 | 0.75 | 0.87 | 51 | empty |
| 3 | 639 | 0.72 | 0.79 | 90 | empty |
| 4 | 245 | 0.63 | 0.81 | 31 | empty |
| 5 | 239 | 0.52 | 0.76 | 36 | GB6 |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3DDF · 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 3DDF · PDBe 3DDF · UniProt Q24451
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.