MolNFT v1 · #34357 · protein
Crystal structure of acyl-CoA oxidase complexed with 3-oh-dodecanoate
2DDH: “Crystal structure of acyl-CoA oxidase complexed with 3-oh-dodecanoate”. X-ray diffraction, 2 ligands (FAD, HXD), 7 pockets (best druggability 0.83). MolNFT v1 #34357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DDH
- Type
- protein
- Length
- 622 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA oxidase
- EC
- 1.3.3.6
- UniProt
- P07872
- Ligands
- FAD, HXD
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA oxidase (EC 1.3.3.6) | protein | 622 | 61% helix, 10% strand | P07872 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- HXD · (3R)-3-hydroxydodecanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.83 | 0.84 | 100 | FAD, HXD |
| 2 | 176 | 0.55 | 0.80 | 26 | empty |
| 3 | 102 | 0.42 | 0.77 | 16 | empty |
| 4 | 58 | 0.40 | 0.80 | 16 | empty |
| 5 | 75 | 0.34 | 0.75 | 13 | empty |
Compared structures
- 2DDH · Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate · the same entry in another collection · chain A against A, TM-score 1.00
- P07872 · AlphaFold monomer V2.0 prediction for peroxisomal acyl-coenzyme a oxidase 1 (P07872) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P07872
- Elsewhere: RCSB PDB 2DDH · PDBe 2DDH · UniProt P07872
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