Research workbench
T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate
Analyse T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SOW
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Toxoplasma gondii
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q27797
- Ligands
- OXL, NAD
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 322 | 51% helix, 19% strand | Q27797 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 323 | 50% helix, 19% strand | Q27797 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.69 | 0.85 | 44 | OXL, NAD |
| 2 | 254 | 0.68 | 0.84 | 43 | OXL, NAD |
| 3 | 167 | 0.53 | 0.79 | 26 | empty |
| 4 | 152 | 0.50 | 0.79 | 25 | empty |
| 5 | 106 | 0.47 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1620 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1SOW · T. gondii bradyzoite-specific ldh (LDH2) in complex with NAD and oxalate · the same entry in another collection · chain A against A, TM-score 1.00
- Q27797 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (Q27797) · a predicted model of the same protein · chain A 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 Q27797
- Elsewhere: RCSB PDB 1SOW · PDBe 1SOW · UniProt Q27797
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