Research workbench
Catabolism of the cholesterol side chain in mycobacterium tuberculosis is controlled by a redox-sensitive thiol switch
Analyse Catabolism of the cholesterol side chain in mycobacterium tuberculosis is… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ONC
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid 3-ketoacyl-CoA thiolase
- EC
- 2.3.1.16
- UniProt
- I6XHI4
- Ligands
- CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Steroid 3-ketoacyl-CoA thiolase (EC 2.3.1.16) | protein | 366 | 39% helix, 24% strand | I6XHI4 |
| B | Steroid 3-ketoacyl-CoA thiolase (EC 2.3.1.16) | protein | 359 | 39% helix, 21% strand | I6XHI4 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.72 | 0.81 | 59 | empty |
| 2 | 349 | 0.69 | 0.82 | 49 | empty |
| 3 | 223 | 0.53 | 0.77 | 33 | empty |
| 4 | 172 | 0.50 | 0.77 | 34 | empty |
| 5 | 103 | 0.43 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2121 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5ONC · Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis is Controlled by a… · the same entry in another collection · chain A against A, TM-score 1.00
- I6XHI4 · AlphaFold monomer V2.0 prediction for steroid 3-ketoacyl-CoA thiolase (I6XHI4) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 I6XHI4
- Elsewhere: RCSB PDB 5ONC · PDBe 5ONC · UniProt I6XHI4
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