Research workbench
Crystal structure of caib, a type III CoA transferase in carnitine metabolism
Analyse Crystal structure of caib, a type III CoA transferase in carnitine metabolism in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XA3
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crotonobetainyl-COA:CARNITINE CoA-transferase
- EC
- 2.8.3.-
- UniProt
- P31572
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Crotonobetainyl-COA:CARNITINE CoA-transferase (EC 2.8.3.-) | protein | 400 | 39% helix, 18% strand | P31572 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.74 | 0.80 | 50 | BTB |
| 2 | 661 | 0.74 | 0.80 | 67 | SO4, BTB |
| 3 | 119 | 0.48 | 0.79 | 19 | empty |
| 4 | 78 | 0.42 | 0.79 | 17 | empty |
| 5 | 104 | 0.40 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 6377 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 1XA3 · Crystal structure of CaiB, a type III CoA transferase in carnitine metabolism · the same entry in another collection · chain A against A, TM-score 1.00
- P31572 · AlphaFold monomer V2.0 prediction for L-carnitine CoA-transferase (P31572) · a predicted model of the same protein · chain B 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 P31572
- Elsewhere: RCSB PDB 1XA3 · PDBe 1XA3 · UniProt P31572
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