Research workbench
Crystal structure of HDHHS20 bound to palmitoyl CoA
Analyse Crystal structure of HDHHS20 bound to palmitoyl CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHM
- Type
- protein
- Length
- 577 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 4 of palmitoyltransferase ZDHHC20
- EC
- 2.3.1.225, 2.3.1.-
- UniProt
- Q5W0Z9
- Ligands
- PKZ, ZN, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 4 of palmitoyltransferase ZDHHC20 (EC 2.3.1.225, 2.3.1.-) | protein | 290 | 58% helix, 8% strand | Q5W0Z9 |
| B | Isoform 4 of palmitoyltransferase ZDHHC20 (EC 2.3.1.225, 2.3.1.-) | protein | 287 | 54% helix, 8% strand | Q5W0Z9 |
Ligands and binding sites
- PKZ · Palmitoyl-CoA · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.75 | 0.95 | 23 | empty |
| 2 | 446 | 0.73 | 0.82 | 47 | empty |
| 3 | 520 | 0.69 | 0.79 | 43 | PKZ, PO4 |
| 4 | 110 | 0.41 | 0.76 | 18 | empty |
| 5 | 57 | 0.40 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q5W0Z9
- Elsewhere: RCSB PDB 7KHM · PDBe 7KHM · UniProt Q5W0Z9
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