Research workbench
Structure of human DHHC20 palmitoyltransferase, space group P63
Analyse Structure of human DHHC20 palmitoyltransferase, space group P63 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BMN
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human DHHC20 palmitoyltransferase
- EC
- 2.3.1.225
- UniProt
- Q5W0Z9
- Ligands
- PAP, ZN, PO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human DHHC20 palmitoyltransferase (EC 2.3.1.225) | protein | 289 | 58% helix, 8% strand | Q5W0Z9 |
| B | Human DHHC20 palmitoyltransferase (EC 2.3.1.225) | protein | 294 | 58% helix, 8% strand | Q5W0Z9 |
Ligands and binding sites
- PAP · 3'-phosphate-adenosine-5'-diphosphate · ligand · chains B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.73 | 0.90 | 25 | empty |
| 2 | 209 | 0.70 | 0.86 | 30 | empty |
| 3 | 499 | 0.63 | 0.75 | 46 | empty |
| 4 | 79 | 0.40 | 0.79 | 19 | PO4 |
| 5 | 55 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6BMN · Structure of human DHHC20 palmitoyltransferase, space group P63 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5W0Z9 · AlphaFold monomer V2.0 prediction for palmitoyltransferase ZDHHC20 (Q5W0Z9) · 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 Q5W0Z9
- Elsewhere: RCSB PDB 6BMN · PDBe 6BMN · UniProt Q5W0Z9
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