MolNFT v1 · #16718 · protein
The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation
1O7D · Lysosomal alpha-mannosidase: “The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.82). MolNFT v1 #16718…
- PDB
- 1O7D
- Type
- protein
- Length
- 893 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosomal alpha-mannosidase
- EC
- 3.2.1.24
- UniProt
- Q29451
- Ligands
- NAG, MAN, BMA, ZN, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosomal alpha-mannosidase (EC 3.2.1.24) | protein | 291 | 40% helix, 14% strand | Q29451 |
| B | Lysosomal alpha-mannosidase (EC 3.2.1.24) | protein | 75 | 48% helix, 13% strand | Q29451 |
| C | Lysosomal alpha-mannosidase (EC 3.2.1.24) | protein | 150 | 31% helix, 33% strand | Q29451 |
| D | Lysosomal alpha-mannosidase (EC 3.2.1.24) | protein | 269 | 9% helix, 45% strand | Q29451 |
| E | Lysosomal alpha-mannosidase (EC 3.2.1.24) | protein | 108 | 3% helix, 44% strand | Q29451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, C, D, A
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C, A, D
- BMA · beta-D-mannopyranose · sugar · chains C
- ZN · Zinc ion · metal · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.82 | 0.83 | 91 | NAG |
| 2 | 213 | 0.57 | 0.80 | 25 | empty |
| 3 | 203 | 0.54 | 0.78 | 35 | empty |
| 4 | 73 | 0.54 | 0.86 | 25 | empty |
| 5 | 76 | 0.36 | 0.76 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2728 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1740 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1670 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1259 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1190 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 1O7D · The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH… · the same entry in another collection · chain E against E, TM-score 1.00
- Q29451 · AlphaFold monomer V2.0 prediction for lysosomal alpha-mannosidase (Q29451) · 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 Q29451
- Elsewhere: RCSB PDB 1O7D · PDBe 1O7D · UniProt Q29451
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