MolNFT v1 · #75069 · protein
Crystal structure of an acyl-CoA dehydrogenase from mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion sad mr
3PFD: “Crystal structure of an acyl-CoA dehydrogenase from mycobacterium thermoresistibile bound to reduced flavin…”. X-ray diffraction, 2 ligands (FDA, IOD), 17 pockets (best druggability 0.83). MolNFT v1 #75069 on GenesisL1: 3D…
- PDB
- 3PFD
- Type
- protein
- Length
- 1,474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.99.3
- Ligands
- FDA, IOD
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-CoA dehydrogenase (EC 1.3.99.3) | protein | 368 | 58% helix, 17% strand | — |
| C | Acyl-CoA dehydrogenase (EC 1.3.99.3) | protein | 369 | 59% helix, 17% strand | — |
| D | Acyl-CoA dehydrogenase (EC 1.3.99.3) | protein | 369 | 58% helix, 17% strand | — |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
- IOD · Iodide ion · ion · 109 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.83 | 0.88 | 61 | FDA, IOD |
| 2 | 632 | 0.83 | 0.87 | 68 | FDA, IOD |
| 3 | 590 | 0.82 | 0.87 | 64 | FDA, IOD |
| 4 | 624 | 0.82 | 0.87 | 65 | FDA, IOD |
| 5 | 941 | 0.81 | 0.83 | 83 | IOD |
Interfaces
6 interfaces between chains.
- A–B · 1967 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1959 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1368 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1351 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3PFD · Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound… · 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 3PFD · PDBe 3PFD
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