MolNFT v1 · #144207 · protein
Structure of human DHHC20 palmitoyltransferase, space group P21
6BMM: “Structure of human DHHC20 palmitoyltransferase, space group P21”. X-ray diffraction, 4 ligands (DYD, OLB, ZN), 6 pockets (best druggability 0.75). MolNFT v1 #144207 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BMM
- Type
- protein
- Length
- 580 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
- DYD, OLB, ZN, PO4
- Pockets
- 6 · best druggability 0.75
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 | 290 | 58% helix, 8% strand | Q5W0Z9 |
| B | Human DHHC20 palmitoyltransferase (EC 2.3.1.225) | protein | 290 | 58% helix, 8% strand | Q5W0Z9 |
Ligands and binding sites
- DYD · (2S,5S)-hexane-2,5-diol · ligand · 6 copies · chains A, B
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.75 | 0.92 | 26 | OLB |
| 2 | 160 | 0.72 | 0.89 | 24 | OLB |
| 3 | 187 | 0.43 | 0.73 | 26 | DYD |
| 4 | 60 | 0.36 | 0.77 | 14 | empty |
| 5 | 100 | 0.34 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 132 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6BMM · Structure of human DHHC20 palmitoyltransferase, space group P21 · 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 B against A, TM-score 0.99
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 6BMM · PDBe 6BMM · UniProt Q5W0Z9
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