MolNFT v1 · #146952 · protein
Human N-acylethanolamine-hydrolyzing acid amidase (naaa) in complex with non-covalent benzothiazole-piperazine inhibitor ARN19702, in presence of triton X-100
6DXX · N-acylethanolamine-hydrolyzing acid amidase subunit alpha: “Human N-acylethanolamine-hydrolyzing acid amidase (naaa) in complex with non-covalent…”. X-ray diffraction, 5 ligands (TON, WTF, NAG), 14 pockets (best druggability 0.78).…
- PDB
- 6DXX
- Type
- protein
- Length
- 984 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylethanolamine-hydrolyzing acid amidase subunit alpha; N-acylethanolamine-hydrolyzing…
- EC
- 3.5.1.60
- UniProt
- Q02083
- Ligands
- TON, WTF, NAG, CL, SCN
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | N-acylethanolamine-hydrolyzing acid amidase subunit alpha (EC 3.5.1.60) | protein | 97 | 63% helix, 6% strand | Q02083 |
| B, D, F | N-acylethanolamine-hydrolyzing acid amidase subunit beta (EC 3.5.1.60) | protein | 231 | 28% helix, 34% strand | Q02083 |
Ligands and binding sites
- TON · 2-{2-[4-(1,1,3,3-tetramethylbutyl) phenoxy]ethoxy}ethanol · ligand · 3 copies · chains A, B, C, D, E, F
- WTF · [2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone · ligand · 3 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, D, C, E, F
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F
- SCN · Thiocyanate ion · ion · 6 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.78 | 0.87 | 48 | CL, WTF |
| 2 | 380 | 0.78 | 0.87 | 44 | SCN, WTF |
| 3 | 351 | 0.77 | 0.88 | 49 | CL, WTF |
| 4 | 194 | 0.75 | 0.90 | 21 | TON |
| 5 | 187 | 0.74 | 0.89 | 21 | TON |
Interfaces
7 interfaces between chains.
- A–B · 2158 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2070 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1999 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 596 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 376 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DXX · Human N-acylethanolamine-hydrolyzing acid amidase (NAAA) in complex with non-covalent… · the same entry in another collection · chain F against F, TM-score 1.00
- Q02083 · AlphaFold monomer V2.0 prediction for N-acylethanolamine-hydrolyzing acid amidase (Q02083) · 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 Q02083
- Elsewhere: RCSB PDB 6DXX · PDBe 6DXX · UniProt Q02083
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