MolNFT v1 · #107489 · protein
Structure of the C93S variant of the 3-ketoacyl-CoA thiolase FADA5 from M. tuberculosis in complex with a steroid and CoA.
4UBT · Acetyl-CoA acetyltransferase FADA5: “Structure of the C93S variant of the 3-ketoacyl-CoA thiolase FADA5 from M. tuberculosis in complex with a…”. X-ray diffraction, 4 ligands (COA, 3G6, NA), 12 pockets (best druggability 0.76).…
- PDB
- 4UBT
- Type
- protein
- Length
- 1,555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase FADA5
- EC
- 2.3.1.16
- UniProt
- I6XHI4
- Ligands
- COA, 3G6, NA, CL
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA acetyltransferase FADA5 (EC 2.3.1.16) | protein | 396 | 38% helix, 23% strand | I6XHI4 |
| B | Acetyl-CoA acetyltransferase FADA5 (EC 2.3.1.16) | protein | 392 | 39% helix, 23% strand | I6XHI4 |
| C | Acetyl-CoA acetyltransferase FADA5 (EC 2.3.1.16) | protein | 391 | 39% helix, 23% strand | I6XHI4 |
| D | Acetyl-CoA acetyltransferase FADA5 (EC 2.3.1.16) | protein | 376 | 39% helix, 24% strand | I6XHI4 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- 3G6 · (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]propanoic acid (non-preferred name) · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.76 | 0.79 | 96 | CL, GOL |
| 2 | 526 | 0.74 | 0.82 | 58 | COA, 3G6 |
| 3 | 538 | 0.74 | 0.82 | 59 | COA, 3G6 |
| 4 | 441 | 0.66 | 0.79 | 48 | 3G6, COA |
| 5 | 318 | 0.63 | 0.80 | 44 | COA, CL |
Interfaces
4 interfaces between chains.
- A–B · 2543 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 542 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 370 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UBT · Structure of the C93S variant of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis… · the same entry in another collection · chain D against D, 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 D 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 4UBT · PDBe 4UBT · UniProt I6XHI4
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