Research workbench
Structure of mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with oxidized nicotinamide adenine dinucleotide
Analyse Structure of mycobacterium tuberculosis beta-oxidation trifunctional enzyme in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4V
- Type
- protein
- Length
- 2,260 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
- NAD, SO4
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) | protein | 729 | 51% helix, 12% strand | O53872 |
| D, C | Putative acyltransferase RV0859 (EC 2.3.1.-) | protein | 401 | 38% helix, 20% strand | O53871 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 25 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.80 | 0.82 | 90 | empty |
| 2 | 491 | 0.77 | 0.85 | 52 | empty |
| 3 | 902 | 0.75 | 0.78 | 75 | NAD |
| 4 | 838 | 0.73 | 0.78 | 71 | NAD |
| 5 | 617 | 0.73 | 0.80 | 72 | empty |
Interfaces
5 interfaces between chains.
- D–C · 2535 Ų buried · 47 hydrogen bonds · protein-protein
- C–A · 1237 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1221 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 554 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7O4V · Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- O53871 · AlphaFold monomer V2.0 prediction for putative acyltransferase RV0859 (O53871) · a predicted model of the same protein · chain D 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 7O4V · PDBe 7O4V · UniProt O53872 · UniProt O53871
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