MolNFT v1 · #146958 · protein
Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (naaa) ortholog
6DY3 · N-acylethanolamine-hydrolyzing acid amidase alpha-subunit: “Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (naaa) ortholog”. X-ray diffraction, 2 ligands (NAG, FUC), 16 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 6DY3
- Type
- protein
- Length
- 1,342 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylethanolamine-hydrolyzing acid amidase alpha-subunit; N-acylethanolamine-hydrolyzing…
- EC
- 3.5.1.60
- UniProt
- Q9GUI1
- Ligands
- NAG, FUC
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | N-acylethanolamine-hydrolyzing acid amidase alpha-subunit (EC 3.5.1.60) | protein | 102 | 58% helix, 6% strand | Q9GUI1 |
| B, D, F, H | N-acylethanolamine-hydrolyzing acid amidase beta-subunit | protein | 234 | 31% helix, 32% strand | Q9GUI1 |
| E | N-acylethanolamine-hydrolyzing acid amidase alpha-subunit (EC 3.5.1.60) | protein | 100 | 62% helix, 7% strand | Q9GUI1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, E, F
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.71 | 0.90 | 34 | empty |
| 2 | 53 | 0.69 | 0.97 | 16 | empty |
| 3 | 142 | 0.69 | 0.89 | 34 | empty |
| 4 | 252 | 0.66 | 0.83 | 54 | empty |
| 5 | 518 | 0.66 | 0.77 | 49 | empty |
Interfaces
16 interfaces between chains.
- C–D · 2688 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2542 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2527 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2512 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 386 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 6DY3 · Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (NAAA) ortholog · the same entry in another collection · chain H against H, TM-score 1.00
- Q9GUI1 · AlphaFold monomer V2.0 prediction for N-acylethanolamine-hydrolyzing acid amidase (Q9GUI1) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9GUI1
- Elsewhere: RCSB PDB 6DY3 · PDBe 6DY3 · UniProt Q9GUI1
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