MolNFT v1 · #118346 · protein
Crystal structure acyl-CoA dehydrogenase from brucella melitensis in complex with FAD
5EZ3: “Crystal structure acyl-CoA dehydrogenase from brucella melitensis in complex with FAD”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.89). MolNFT v1 #118346 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5EZ3
- Type
- protein
- Length
- 2,163 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.8.-
- UniProt
- Q8YC61
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 1.3.8.-) | protein | 540 | 59% helix, 14% strand | Q8YC61 |
| B, C, D | Acyl-CoA dehydrogenase (EC 1.3.8.-) | protein | 541 | 57% helix, 14% strand | Q8YC61 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 7 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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 | 898 | 0.89 | 0.91 | 119 | FAD, MRD |
| 2 | 922 | 0.88 | 0.90 | 135 | FAD, MRD |
| 3 | 766 | 0.86 | 0.90 | 101 | FAD, MRD |
| 4 | 713 | 0.86 | 0.90 | 100 | FAD, MRD |
| 5 | 187 | 0.76 | 0.92 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4018 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 3992 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 904 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 855 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5EZ3 · Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD · 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 Q8YC61
- Elsewhere: RCSB PDB 5EZ3 · PDBe 5EZ3 · UniProt Q8YC61
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.