MolNFT v1 · #127970 · protein
Structure of fatty acid photodecarboxylase in complex with FAD and palmitic acid
5NCC: “Structure of fatty acid photodecarboxylase in complex with FAD and palmitic acid”. X-ray diffraction, 2 ligands (FAD, PLM), 20 pockets (best druggability 0.89). MolNFT v1 #127970 on GenesisL1: 3D structure, binding sites and pockets…
- 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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