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Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex Octanoyl coenzyme A
Analyse Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PCD
- Type
- protein
- Length
- 1,594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.37
- Source
- Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
- Molecule
- Beta-ketoadipyl-CoA thiolase
- EC
- 2.3.1.16, 2.3.1.174
- UniProt
- Q88N39
- Ligands
- OYA, COA, K, CL
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.37 · 4 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 | 401 | 39% helix, 22% strand | Q88N39 |
| B | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 394 | 40% helix, 21% strand | Q88N39 |
| C | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 397 | 40% helix, 22% strand | Q88N39 |
| D | Beta-ketoadipyl-CoA thiolase (EC 2.3.1.16, 2.3.1.174) | protein | 402 | 39% helix, 22% strand | Q88N39 |
Ligands and binding sites
- OYA · Octanal · ligand · 3 copies · chains A, D, B, C
- COA · Coenzyme A · ligand · 2 copies · chains A, D
- K · Potassium ion · metal · 3 copies · chains B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.70 | 0.86 | 41 | OYA |
| 2 | 271 | 0.69 | 0.84 | 50 | COA, OYA |
| 3 | 263 | 0.68 | 0.84 | 44 | OYA |
| 4 | 242 | 0.68 | 0.85 | 42 | CL, GOL |
| 5 | 109 | 0.44 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3522 Ų buried · 87 hydrogen bonds · protein-protein
- B–C · 3364 Ų buried · 86 hydrogen bonds · protein-protein
- C–D · 727 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6PCD · Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex octanoyl… · 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 6PCD · PDBe 6PCD · UniProt Q88N39
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