Research workbench
Golgi alpha-mannosidase II in complex with mannostatin a at pH 5.75
Analyse Golgi alpha-mannosidase II in complex with mannostatin a at pH 5.75 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DX0
- 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
- MSN, NAG, ZN, SO4
- 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
- MSN · (1R,2R,3R,4S,5R)-4-amino-5-(methylthio)cyclopentane-1,2,3-triol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 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 | 136 | 0.80 | 0.98 | 30 | empty |
| 2 | 318 | 0.75 | 0.87 | 51 | empty |
| 3 | 622 | 0.72 | 0.80 | 88 | SO4 |
| 4 | 271 | 0.63 | 0.81 | 32 | empty |
| 5 | 247 | 0.54 | 0.77 | 34 | MSN |
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3DX0 · Golgi alpha-Mannosidase II in complex with Mannostatin A at pH 5.75 · 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 3DX0 · PDBe 3DX0 · UniProt Q24451
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