Research workbench
Crystal structure of fatty acid photodecarboxylase in the dark state determined by serial femtosecond crystallography at room temperature
Analyse Crystal structure of fatty acid photodecarboxylase in the dark state determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZH7
- Type
- protein
- Length
- 1,125 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid photodecarboxylase, chloroplastic
- EC
- 4.1.1.106
- UniProt
- A0A248QE08
- Ligands
- STE, FAD
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty acid photodecarboxylase, chloroplastic (EC 4.1.1.106) | protein | 563 | 29% helix, 22% strand | A0A248QE08 |
| B | Fatty acid photodecarboxylase, chloroplastic (EC 4.1.1.106) | protein | 562 | 30% helix, 22% strand | A0A248QE08 |
Ligands and binding sites
- STE · Stearic acid · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.88 | 0.94 | 97 | FAD, STE |
| 2 | 558 | 0.87 | 0.93 | 101 | FAD, STE |
| 3 | 386 | 0.64 | 0.79 | 45 | empty |
| 4 | 90 | 0.56 | 0.85 | 17 | STE |
| 5 | 96 | 0.55 | 0.84 | 17 | STE |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZH7 · Crystal structure of fatty acid photodecarboxylase in the dark state determined by serial… · the same entry in another collection · 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 A0A248QE08
- Elsewhere: RCSB PDB 6ZH7 · PDBe 6ZH7 · UniProt A0A248QE08
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