MolNFT v1 · #103558 · protein
Crystal structure of patatin-17 complexed with methyl arachidonyl fluorophosphonate (mafp)
4PKB: “Crystal structure of patatin-17 complexed with methyl arachidonyl fluorophosphonate (mafp)”. X-ray diffraction, 1 ligand (MAY), 5 pockets (best druggability 0.72). MolNFT v1 #103558 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PKB
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Patatin-17
- EC
- 3.1.1.-
- UniProt
- Q8LPW4
- Ligands
- MAY
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Patatin-17 (EC 3.1.1.-) | protein | 357 | 49% helix, 16% strand | Q8LPW4 |
Ligands and binding sites
- MAY · Methyl arachidonyl fluorophosphonate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.98 | 27 | MAY |
| 2 | 169 | 0.62 | 0.84 | 27 | empty |
| 3 | 163 | 0.48 | 0.77 | 24 | empty |
| 4 | 69 | 0.30 | 0.73 | 17 | empty |
| 5 | 65 | 0.25 | 0.71 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4PKB · Crystal structure of patatin-17 complexed with methyl arachidonyl fluorophosphonate (mafp) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8LPW4 · AlphaFold monomer V2.0 prediction for patatin-17 (Q8LPW4) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q8LPW4
- Elsewhere: RCSB PDB 4PKB · PDBe 4PKB · UniProt Q8LPW4
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