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The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent substrate specificities of the two lysosomal thioesterases (PPT1 and PPT2)
Analyse The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJA
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoyl-protein thioesterase 2 precursor
- EC
- 3.1.2.22
- UniProt
- Q9UMR5
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoyl-protein thioesterase 2 precursor (EC 3.1.2.22) | protein | 268 | 44% helix, 14% strand | Q9UMR5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.63 | 0.86 | 24 | GOL |
| 2 | 118 | 0.40 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1PJA · The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UMR5 · AlphaFold monomer V2.0 prediction for lysosomal thioesterase PPT2 (Q9UMR5) · 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 Q9UMR5
- Elsewhere: RCSB PDB 1PJA · PDBe 1PJA · UniProt Q9UMR5
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