Research workbench
T. gondii bradyzoite-specific ldh (LDH2) in complex with NAD and oxq
Analyse T. gondii bradyzoite-specific ldh (LDH2) in complex with NAD and oxq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZM
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q27797
- Ligands
- NAD, OXQ
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 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
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- OXQ · 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.72 | 0.86 | 44 | NAD, OXQ |
| 2 | 260 | 0.69 | 0.85 | 42 | NAD, OXQ |
| 3 | 175 | 0.52 | 0.79 | 31 | empty |
| 4 | 141 | 0.50 | 0.80 | 27 | empty |
| 5 | 83 | 0.39 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1629 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3CZM · T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ · 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 3CZM · PDBe 3CZM · UniProt Q27797
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