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Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like protein (NAALADaseL)
Analyse Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TWE
- Type
- protein
- Length
- 1,412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Homo sapiens
- Molecule
- N-acetylated-alpha-linked acidic dipeptidase-like protein
- EC
- 3.4.17.21
- UniProt
- Q9UQQ1
- Ligands
- NAG, BMA, ZN, CA
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.75 · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylated-alpha-linked acidic dipeptidase-like protein (EC 3.4.17.21) | protein | 706 | 38% helix, 17% strand | Q9UQQ1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.85 | 0.93 | 54 | empty |
| 2 | 862 | 0.72 | 0.77 | 91 | ZN, PEG |
| 3 | 672 | 0.68 | 0.76 | 60 | PEG |
| 4 | 268 | 0.68 | 0.83 | 42 | GOL |
| 5 | 207 | 0.66 | 0.85 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2480 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4TWE · Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UQQ1 · AlphaFold monomer V2.0 prediction for aminopeptidase NAALADL1 (Q9UQQ1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UQQ1
- Elsewhere: RCSB PDB 4TWE · PDBe 4TWE · UniProt Q9UQQ1
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