Research workbench
Crystal structure of mouse SCD1 with a diiron center
Analyse Crystal structure of mouse SCD1 with a diiron center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WF2
- Type
- protein
- Length
- 633 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
- 3VV, FE
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA desaturase 1 (EC 1.14.19.1) | protein | 321 | 59% helix, 3% strand | P13516 |
| B | Acyl-CoA desaturase 1 (EC 1.14.19.1) | protein | 312 | 60% helix, 3% strand | P13516 |
Ligands and binding sites
- 3VV · S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3, 5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2, 4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.72 | 0.83 | 53 | 3VV |
| 2 | 359 | 0.71 | 0.83 | 43 | 3VV |
| 3 | 229 | 0.56 | 0.78 | 32 | empty |
| 4 | 93 | 0.51 | 0.83 | 19 | empty |
| 5 | 53 | 0.50 | 0.87 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 4 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 6WF2 · PDBe 6WF2 · UniProt P13516
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