MolNFT v1 · #134300 · protein
Novel structural insights into GDP-mediated regulation of acyl-CoA thioesterases
5SZY · Acyl-CoA hydrolase: “Novel structural insights into GDP-mediated regulation of acyl-CoA thioesterases”. X-ray diffraction, 3 ligands (GDP, COA, CL), 13 pockets (best druggability 0.60). MolNFT v1 #134300 on GenesisL1: 3D structure…
- PDB
- 5SZY
- Type
- protein
- Length
- 592 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
- GDP, COA, CL
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 149 | 28% helix, 38% strand | A0A0Y5D4F5 |
| B | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 147 | 28% helix, 39% strand | A0A0Y5D4F5 |
| C, D | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 148 | 28% helix, 38% strand | A0A0Y5D4F5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.60 | 0.84 | 25 | CL |
| 2 | 162 | 0.60 | 0.83 | 23 | CL |
| 3 | 81 | 0.51 | 0.84 | 19 | empty |
| 4 | 190 | 0.50 | 0.77 | 23 | GDP |
| 5 | 158 | 0.49 | 0.78 | 27 | GDP |
Interfaces
3 interfaces between chains.
- A–C · 1342 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1139 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 664 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5SZY · 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 5SZY · PDBe 5SZY · UniProt A0A0Y5D4F5
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