Research workbench
Crystal structure of stearoyl-coenzyme a desaturase 1
Analyse Crystal structure of stearoyl-coenzyme a desaturase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YMK
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA desaturase 1
- EC
- 1.14.19.1
- UniProt
- P13516
- Ligands
- ST9, MPG, ZN
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA desaturase 1 (EC 1.14.19.1) | protein | 322 | 58% helix, 3% strand | P13516 |
| D | Acyl-CoA desaturase 1 (EC 1.14.19.1) | protein | 312 | 58% helix, 3% strand | P13516 |
Ligands and binding sites
- ST9 · Stearoyl-coenzyme A · ligand · 2 copies · chains A, D
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.73 | 0.83 | 50 | ST9 |
| 2 | 378 | 0.73 | 0.84 | 45 | ST9 |
| 3 | 185 | 0.61 | 0.82 | 31 | empty |
| 4 | 165 | 0.53 | 0.79 | 24 | empty |
| 5 | 50 | 0.52 | 0.88 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 449 Ų buried · 6 hydrogen bonds · 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 P13516
- Elsewhere: RCSB PDB 4YMK · PDBe 4YMK · UniProt P13516
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