Research workbench
Structure of mycobacterium tuberculosis beta-oxidation trifunctional enzyme with coenzyme a bound at the hydratase, thiolase active sites and additional binding site (COA(ECH2))
Analyse Structure of mycobacterium tuberculosis beta-oxidation trifunctional enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4S
- Type
- protein
- Length
- 2,261 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase; Putative acyltransferase RV0859
- EC
- 1.1.1.35, 2.3.1.-
- UniProt
- O53872, O53871
- Ligands
- COA, PAP, ADP, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 729 | 50% helix, 13% strand | O53872 |
| B | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 728 | 51% helix, 13% strand | O53872 |
| C, D | Putative acyltransferase RV0859 (EC 2.3.1.-) | protein | 402 | 42% helix, 20% strand | O53871 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D
- PAP · 3'-phosphate-adenosine-5'-diphosphate · ligand · chains B, C
- ADP · Adenosine-5'-diphosphate · ligand · chains A, D
- SO4 · Sulfate ion · ion · 26 copies · chains A, C, D, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.77 | 0.80 | 79 | empty |
| 2 | 1007 | 0.77 | 0.79 | 105 | empty |
| 3 | 860 | 0.76 | 0.79 | 77 | empty |
| 4 | 579 | 0.72 | 0.80 | 60 | COA |
| 5 | 380 | 0.70 | 0.82 | 53 | COA, GOL |
Interfaces
5 interfaces between chains.
- C–D · 2454 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1158 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1150 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 579 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7O4S · Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme… · the same entry in another collection · chain A against A, TM-score 1.00
- O53871 · AlphaFold monomer V2.0 prediction for putative acyltransferase RV0859 (O53871) · 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 O53872
- Every structure of UniProt O53871
- Elsewhere: RCSB PDB 7O4S · PDBe 7O4S · UniProt O53872 · UniProt O53871
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