MolNFT v1 · #160159 · protein
Crystal structure of beta-ketoadipyl-CoA thiolase
6PCA: “Crystal structure of beta-ketoadipyl-CoA thiolase”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.63). MolNFT v1 #160159 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PCA
- Type
- protein
- Length
- 1,599 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-ketoadipyl-CoA thiolase
- EC
- 2.3.1.16, 2.3.1.174
- UniProt
- Q88N39
- Ligands
- CL
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 397 | 39% helix, 22% strand | Q88N39 |
| B, C | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 403 | 38% helix, 22% strand | Q88N39 |
| D | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 396 | 39% helix, 21% strand | Q88N39 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, D, B, C
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.63 | 0.85 | 37 | GOL, CL |
| 2 | 191 | 0.62 | 0.83 | 40 | CL, GOL |
| 3 | 215 | 0.62 | 0.82 | 40 | CL, GOL |
| 4 | 179 | 0.61 | 0.83 | 35 | GOL, CL |
| 5 | 97 | 0.45 | 0.80 | 19 | ACT |
Interfaces
6 interfaces between chains.
- B–C · 3465 Ų buried · 92 hydrogen bonds · protein-protein
- A–D · 3327 Ų buried · 81 hydrogen bonds · protein-protein
- C–D · 715 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 713 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PCA · Crystal structure of beta-ketoadipyl-CoA thiolase · 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 Q88N39
- Elsewhere: RCSB PDB 6PCA · PDBe 6PCA · UniProt Q88N39
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