Research workbench
Crystal structure of rat carnitine palmitoyltransferase 2 in space group C2221
Analyse Crystal structure of rat carnitine palmitoyltransferase 2 in space group C2221 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DEB
- Type
- protein
- Length
- 1,253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carnitine O-palmitoyltransferase II, mitochondrial
- EC
- 2.3.1.21
- UniProt
- P18886
- Ligands
- COA, PLM
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carnitine O-palmitoyltransferase II, mitochondrial (EC 2.3.1.21) | protein | 627 | 47% helix, 15% strand | P18886 |
| B | Carnitine O-palmitoyltransferase II, mitochondrial (EC 2.3.1.21) | protein | 626 | 47% helix, 15% strand | P18886 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.81 | 0.83 | 96 | PLM |
| 2 | 1196 | 0.78 | 0.80 | 104 | PLM |
| 3 | 370 | 0.57 | 0.75 | 41 | empty |
| 4 | 50 | 0.55 | 0.90 | 16 | empty |
| 5 | 73 | 0.54 | 0.86 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2DEB · Crystal structure of rat carnitine palmitoyltransferase 2 in space group C2221 · the same entry in another collection · chain A against A, TM-score 1.00
- P18886 · AlphaFold monomer V2.0 prediction for carnitine O-palmitoyltransferase 2, mitochondrial… · 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 P18886
- Elsewhere: RCSB PDB 2DEB · PDBe 2DEB · UniProt P18886
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