MolNFT v1 · #125934 · protein
Crystal structure of mmgc, an acyl-CoA dehydrogenase from bacillus subtilis.
5LNX: “Crystal structure of mmgc, an acyl-CoA dehydrogenase from bacillus subtilis.”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.85). MolNFT v1 #125934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LNX
- Type
- protein
- Length
- 2,958 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.99.-
- UniProt
- P45857
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 367 | 54% helix, 17% strand | P45857 |
| B | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 372 | 57% helix, 17% strand | P45857 |
| C | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 364 | 55% helix, 15% strand | P45857 |
| D | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 374 | 55% helix, 16% strand | P45857 |
| E | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 368 | 56% helix, 16% strand | P45857 |
| F | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 372 | 54% helix, 15% strand | P45857 |
| G | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 367 | 57% helix, 16% strand | P45857 |
| H | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 374 | 56% helix, 17% strand | P45857 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, D, C, E, F, H, G
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.85 | 0.90 | 66 | FAD |
| 2 | 687 | 0.84 | 0.88 | 85 | FAD |
| 3 | 594 | 0.83 | 0.88 | 63 | FAD |
| 4 | 578 | 0.83 | 0.88 | 67 | FAD |
| 5 | 480 | 0.83 | 0.89 | 61 | GOL, FAD |
Interfaces
16 interfaces between chains.
- A–B · 2038 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1954 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1916 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1891 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 1412 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5LNX · Crystal structure of MmgC, an acyl-CoA dehydrogenase from bacillus subtilis. · the same entry in another collection · chain H against H, TM-score 1.00
- P45857 · AlphaFold monomer V2.0 prediction for acyl-CoA dehydrogenase (P45857) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P45857
- Elsewhere: RCSB PDB 5LNX · PDBe 5LNX · UniProt P45857
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