MolNFT v2 · #215770 · protein
Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-B-DNQ
8OPY · 3-hydroxyacyl-CoA dehydrogenase: “Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-B-DNQ”. X-ray diffraction at 2.45, 2 ligands (DNQ, SO4), 19 pockets (best druggability 0.78).…
- PDB
- 8OPY
- Type
- protein
- Length
- 2,253 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Mycobacterium tuberculosis H37Rv
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase; Putative acyltransferase Rv0859
- EC
- 1.1.1.35, 2.3.1.-
- UniProt
- O53872, O53871
- Ligands
- DNQ, SO4
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.45 · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 731 | 51% helix, 13% strand | O53872 |
| B | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 728 | 51% helix, 13% strand | O53872 |
| C | Putative acyltransferase Rv0859 (EC 2.3.1.-) | protein | 395 | 42% helix, 22% strand | O53871 |
| D | Putative acyltransferase Rv0859 (EC 2.3.1.-) | protein | 399 | 39% helix, 20% strand | O53871 |
Ligands and binding sites
- DNQ · 6,7-dinitroquinoxaline-2,3-dione · ligand · 2 copies · chains D
- SO4 · Sulfate ion · ion · 21 copies · chains A, C, D, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.78 | 0.81 | 72 | empty |
| 2 | 725 | 0.76 | 0.81 | 67 | GOL |
| 3 | 716 | 0.76 | 0.81 | 96 | empty |
| 4 | 504 | 0.75 | 0.83 | 54 | empty |
| 5 | 300 | 0.72 | 0.85 | 39 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 2499 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1183 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1126 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 543 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- O53871 · AlphaFold monomer V2.0 prediction for putative acyltransferase RV0859 (O53871) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 8OPY · PDBe 8OPY · UniProt O53872 · UniProt O53871
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