MolNFT v1 · #124049 · protein
Crystal structure of acyl-CoA oxidase-1 in caenorhabditis elegans complexed with FAD and ATP
5K3I · Acyl-coenzyme a oxidase: “Crystal structure of acyl-CoA oxidase-1 in caenorhabditis elegans complexed with FAD and ATP”. X-ray diffraction, 3 ligands (FAD, ATP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #124049 on…
- PDB
- 5K3I
- Type
- protein
- Length
- 5,247 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-coenzyme a oxidase
- UniProt
- O62140
- Ligands
- FAD, ATP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H | Acyl-coenzyme a oxidase | protein | 661 | 58% helix, 9% strand | O62140 |
| B | Acyl-coenzyme a oxidase | protein | 657 | 58% helix, 9% strand | O62140 |
| C | Acyl-coenzyme a oxidase | protein | 650 | 58% helix, 10% strand | O62140 |
| D | Acyl-coenzyme a oxidase | protein | 653 | 58% helix, 9% strand | O62140 |
| F | Acyl-coenzyme a oxidase | protein | 651 | 59% helix, 9% strand | O62140 |
| G | Acyl-coenzyme a oxidase | protein | 653 | 59% helix, 10% strand | O62140 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.88 | 0.90 | 111 | FAD |
| 2 | 1003 | 0.87 | 0.88 | 90 | FAD |
| 3 | 1163 | 0.87 | 0.88 | 114 | FAD |
| 4 | 1139 | 0.87 | 0.88 | 107 | FAD |
| 5 | 1149 | 0.87 | 0.88 | 114 | FAD |
Interfaces
9 interfaces between chains.
- C–D · 6063 Ų buried · 80 hydrogen bonds · protein-protein
- G–H · 6038 Ų buried · 82 hydrogen bonds · protein-protein
- A–B · 6036 Ų buried · 77 hydrogen bonds · protein-protein
- E–F · 6019 Ų buried · 76 hydrogen bonds · protein-protein
- C–E · 579 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5K3I · Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and… · the same entry in another collection · chain H against H, TM-score 1.00
- O62140 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase acox-1.1 (O62140) · a predicted model of the same protein · 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 O62140
- Elsewhere: RCSB PDB 5K3I · PDBe 5K3I · UniProt O62140
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