Research workbench
Structure of fatty acid photodecarboxylase in complex with FAD and palmitic acid
Analyse Structure of fatty acid photodecarboxylase in complex with FAD and palmitic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NCC
- Type
- protein
- Length
- 3,468 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid photodecarboxylase
- Ligands
- FAD, PLM
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Fatty acid photodecarboxylase | protein | 578 | 26% helix, 18% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- PLM · Palmitic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.89 | 0.94 | 98 | FAD |
| 2 | 688 | 0.88 | 0.93 | 124 | FAD, PLM |
| 3 | 544 | 0.88 | 0.95 | 87 | FAD, PLM |
| 4 | 571 | 0.88 | 0.94 | 93 | FAD, PLM |
| 5 | 601 | 0.88 | 0.94 | 101 | FAD, PLM |
Interfaces
8 interfaces between chains.
- A–B · 1272 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1185 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1105 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5NCC · Structure of Fatty acid Photodecarboxylase in complex with FAD and palmitic acid · 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
- Elsewhere: RCSB PDB 5NCC · PDBe 5NCC
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