MolNFT v1 · #122052 · protein
Crystal structure of an acyl-CoA dehydrogenase domain protein from burkholderia phymatum bound to FAD
5IDU: “Crystal structure of an acyl-CoA dehydrogenase domain protein from burkholderia phymatum bound to FAD”. X-ray diffraction, 1 ligand (FAD), 12 pockets (best druggability 0.86). MolNFT v1 #122052 on GenesisL1: 3D structure, binding…
- PDB
- 5IDU
- Type
- protein
- Length
- 1,578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase domain protein
- UniProt
- B2JPK4
- Ligands
- FAD
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acyl-CoA dehydrogenase domain protein | protein | 392 | 59% helix, 16% strand | B2JPK4 |
| B | Acyl-CoA dehydrogenase domain protein | protein | 389 | 58% helix, 16% strand | B2JPK4 |
| C | Acyl-CoA dehydrogenase domain protein | protein | 405 | 58% helix, 16% strand | B2JPK4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.86 | 0.91 | 67 | FAD, EDO |
| 2 | 573 | 0.85 | 0.90 | 82 | FAD |
| 3 | 798 | 0.85 | 0.88 | 104 | FAD, EDO |
| 4 | 887 | 0.85 | 0.86 | 90 | FAD, EDO |
| 5 | 451 | 0.62 | 0.76 | 38 | EDO |
Interfaces
6 interfaces between chains.
- B–C · 2152 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1965 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1700 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1686 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5IDU · Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum… · 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 B2JPK4
- Elsewhere: RCSB PDB 5IDU · PDBe 5IDU · UniProt B2JPK4
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