Research workbench
Novel structural insights into GDP-mediated regulation of acyl-CoA thioesterases
Analyse Novel structural insights into GDP-mediated regulation of acyl-CoA thioesterases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V3A
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA hydrolase
- EC
- 3.1.2.-
- UniProt
- A0A0Y5D4F5
- Ligands
- COA, GDP
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 154 | 27% helix, 38% strand | A0A0Y5D4F5 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.77 | 0.79 | 109 | GDP |
| 2 | 1072 | 0.76 | 0.78 | 111 | GDP |
| 3 | 161 | 0.58 | 0.82 | 25 | empty |
| 4 | 158 | 0.58 | 0.82 | 26 | COA |
| 5 | 136 | 0.57 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1484 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 629 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5V3A · Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases · the same entry in another collection · 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 A0A0Y5D4F5
- Elsewhere: RCSB PDB 5V3A · PDBe 5V3A · UniProt A0A0Y5D4F5
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