MolNFT v1 · #73952 · protein
Crystal structure of a putative acyl-CoA dehydrogenase from mycobacterium smegmatis, iodide soak
3OIB: “Crystal structure of a putative acyl-CoA dehydrogenase from mycobacterium smegmatis, iodide soak”. X-ray diffraction, 3 ligands (FDA, NA, IOD), 4 pockets (best druggability 0.83). MolNFT v1 #73952 on GenesisL1: 3D structure, binding…
- PDB
- 3OIB
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- UniProt
- A0R3J1
- Ligands
- FDA, NA, IOD
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-CoA dehydrogenase | protein | 381 | 55% helix, 17% strand | A0R3J1 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 30 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.83 | 0.84 | 102 | IOD, FDA |
| 2 | 1103 | 0.82 | 0.83 | 104 | IOD, FDA |
| 3 | 398 | 0.59 | 0.76 | 49 | IOD |
| 4 | 217 | 0.54 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1787 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3OIB · Crystal structure of a putative ACYL-COA Dehydrogenase from mycobacterium smegmatis… · 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 A0R3J1
- Elsewhere: RCSB PDB 3OIB · PDBe 3OIB · UniProt A0R3J1
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