Research workbench
Rabbit N-acylethanolamine-hydrolyzing acid amidase (naaa) with fatty acid (myristate), in presence of triton X-100
Analyse Rabbit N-acylethanolamine-hydrolyzing acid amidase (naaa) with fatty acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DY1
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylethanolamine acid amidase alpha-subunit; N-acylethanolamine acid amidase…
- EC
- 3.5.1.60
- UniProt
- G1T7U7
- Ligands
- TON, MYR, NAG, CL, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acylethanolamine acid amidase alpha-subunit (EC 3.5.1.60) | protein | 95 | 66% helix, 5% strand | G1T7U7 |
| B | N-acylethanolamine acid amidase beta-subunit (EC 3.5.1.60) | protein | 232 | 25% helix, 34% strand | G1T7U7 |
Ligands and binding sites
- TON · 2-{2-[4-(1,1,3,3-tetramethylbutyl) phenoxy]ethoxy}ethanol · ligand · 2 copies · chains A, B
- MYR · Myristic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.83 | 0.97 | 38 | MYR |
| 2 | 223 | 0.62 | 0.81 | 20 | TON |
| 3 | 117 | 0.36 | 0.73 | 23 | CL |
| 4 | 51 | 0.29 | 0.76 | 10 | CL |
Interfaces
1 interface between chains.
- A–B · 2011 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 6DY1 · Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fatty acid (myristate), in… · the same entry in another collection · chain A against A, TM-score 1.00
- G1T7U7 · AlphaFold monomer V2.0 prediction for N-acylethanolamine-hydrolyzing acid amidase (G1T7U7) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 G1T7U7
- Elsewhere: RCSB PDB 6DY1 · PDBe 6DY1 · UniProt G1T7U7
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