MolNFT v1 · #74710 · protein
Crystal structure of a putative acyl-CoA dehydrogenase from mycobacterium smegmatis
3P4T: “Crystal structure of a putative acyl-CoA dehydrogenase from mycobacterium smegmatis”. X-ray diffraction, 1 ligand (FAO), 4 pockets (best druggability 0.83). MolNFT v1 #74710 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3P4T
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acyl-CoA dehydrogenase
- EC
- 1.1.1.35
- UniProt
- A0R3J1
- Ligands
- FAO
- 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 | Putative acyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 381 | 55% helix, 17% strand | A0R3J1 |
Ligands and binding sites
- FAO · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · 2 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 | 1106 | 0.83 | 0.84 | 100 | FAO |
| 2 | 1042 | 0.83 | 0.84 | 101 | FAO |
| 3 | 364 | 0.58 | 0.76 | 45 | empty |
| 4 | 222 | 0.54 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1849 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3P4T · 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 3P4T · PDBe 3P4T · UniProt A0R3J1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.