MolNFT v1 · #146955 · protein
Rabbit N-acylethanolamine-hydrolyzing acid amidase (naaa) covalently bound to beta-lactam inhibitor ARN726, in presence of triton X-100
6DY0 · N-acylethanolamine acid amidase alpha-subunit: “Rabbit N-acylethanolamine-hydrolyzing acid amidase (naaa) covalently bound to beta-lactam inhibitor ARN726…”. X-ray diffraction, 4 ligands (TON, HJA, NAG), 2 pockets (best druggability…
- PDB
- 6DY0
- Type
- protein
- Length
- 326 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, HJA, NAG, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acylethanolamine acid amidase alpha-subunit (EC 3.5.1.60) | protein | 95 | 65% helix, 5% strand | G1T7U7 |
| B | N-acylethanolamine acid amidase beta-subunit (EC 3.5.1.60) | protein | 231 | 26% helix, 37% strand | G1T7U7 |
Ligands and binding sites
- TON · 2-{2-[4-(1,1,3,3-tetramethylbutyl) phenoxy]ethoxy}ethanol · ligand · 2 copies · chains A, B
- HJA · (2S)-3-amino-2-{[(4-cyclohexylbutoxy) carbonyl]amino}propanethioic S-acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.79 | 0.87 | 46 | HJA |
| 2 | 242 | 0.64 | 0.81 | 21 | TON |
Interfaces
1 interface between chains.
- A–B · 1976 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 covalent (N-glycosylation, covalent ligand).
Compared structures
- 6DY0 · Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam… · 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 6DY0 · PDBe 6DY0 · UniProt G1T7U7
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