MolNFT v1 · #5412 · protein
Crystal structure of palmitoyl protein thioesterase 1 complexed with palmitate
1EH5: “Crystal structure of palmitoyl protein thioesterase 1 complexed with palmitate”. X-ray diffraction, 2 ligands (PLM, NAG), 3 pockets (best druggability 0.53). MolNFT v1 #5412 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1EH5
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoyl protein thioesterase 1
- EC
- 3.1.2.22
- UniProt
- P45478
- Ligands
- PLM, NAG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoyl protein thioesterase 1 (EC 3.1.2.22) | protein | 279 | 41% helix, 14% strand | P45478 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.53 | 0.77 | 34 | PLM |
| 2 | 114 | 0.49 | 0.81 | 23 | empty |
| 3 | 50 | 0.25 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).
Compared structures
- 1EH5 · Crystal structure of palmitoyl protein thioesterase 1 complexed with palmitate · the same entry in another collection · chain A against A, TM-score 1.00
- P45478 · AlphaFold monomer V2.0 prediction for palmitoyl-protein thioesterase 1 (P45478) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P45478
- Elsewhere: RCSB PDB 1EH5 · PDBe 1EH5 · UniProt P45478
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