Research workbench
Crystal structure of mouse carnitine octanoyltransferase in complex with octanoylcarnitine
Analyse Crystal structure of mouse carnitine octanoyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XL8
- Type
- protein
- Length
- 1,191 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal carnitine O-octanoyltransferase
- EC
- 2.3.1.137
- UniProt
- Q9DC50
- Ligands
- 152, OCB
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) | protein | 591 | 47% helix, 15% strand | Q9DC50 |
| B | Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) | protein | 600 | 47% helix, 15% strand | Q9DC50 |
Ligands and binding sites
- 152 · Carnitine · ligand · chains A
- OCB · Octanoylcarnitine · ligand · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.79 | 0.82 | 75 | 152 |
| 2 | 895 | 0.78 | 0.81 | 83 | OCB, MPD |
| 3 | 76 | 0.64 | 0.91 | 17 | empty |
| 4 | 60 | 0.61 | 0.91 | 17 | empty |
| 5 | 122 | 0.60 | 0.86 | 29 | empty |
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 1XL8 · Crystal structure of mouse carnitine octanoyltransferase in complex with octanoylcarnitine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9DC50 · AlphaFold monomer V2.0 prediction for peroxisomal carnitine O-octanoyltransferase (Q9DC50) · a predicted model of the same protein · chain B 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 Q9DC50
- Elsewhere: RCSB PDB 1XL8 · PDBe 1XL8 · UniProt Q9DC50
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