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Structure of a modified C93S variant of the 3-ketoacyl-CoA thiolase FADA5 from M. tuberculosis in complex with CoA
Analyse Structure of a modified C93S variant of the 3-ketoacyl-CoA thiolase FADA5 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UBU
- Type
- protein
- Length
- 3,134 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase FADA5
- UniProt
- I6XHI4
- Ligands
- COA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Acetyl-CoA acetyltransferase FADA5 | protein | 391 | 40% helix, 23% strand | I6XHI4 |
| E | Acetyl-CoA acetyltransferase FADA5 | protein | 392 | 40% helix, 23% strand | I6XHI4 |
| G | Acetyl-CoA acetyltransferase FADA5 | protein | 393 | 40% helix, 23% strand | I6XHI4 |
| H | Acetyl-CoA acetyltransferase FADA5 | protein | 394 | 39% helix, 23% strand | I6XHI4 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 4 copies · chains A, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.74 | 0.78 | 83 | empty |
| 2 | 606 | 0.68 | 0.77 | 68 | empty |
| 3 | 459 | 0.68 | 0.79 | 57 | COA |
| 4 | 869 | 0.68 | 0.74 | 90 | empty |
| 5 | 423 | 0.67 | 0.80 | 57 | COA |
Interfaces
10 interfaces between chains.
- F–H · 2467 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 2393 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2379 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 506 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 406 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 4UBU · Structure of a modified C93S variant of the 3-ketoacyl-CoA thiolase FadA5 from M.… · the same entry in another collection · chain H against H, 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 C 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 I6XHI4
- Elsewhere: RCSB PDB 4UBU · PDBe 4UBU · UniProt I6XHI4
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