Research workbench
Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (L-lactic acid) and cofactor (B- nicotinamide adenine dinucleotide)
Analyse Crystal structure of the lactate dehydrogenase from cryptosporidium parvum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ND3
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5CYZ2
- Ligands
- NAD, 2OP
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase (EC 1.1.1.27) | protein | 317 | 49% helix, 19% strand | Q5CYZ2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.79 | 0.82 | 90 | NAD, 2OP |
| 2 | 76 | 0.62 | 0.91 | 17 | GOL |
| 3 | 75 | 0.58 | 0.88 | 16 | empty |
| 4 | 138 | 0.50 | 0.79 | 24 | empty |
| 5 | 135 | 0.48 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2060 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4ND3 · Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with… · the same entry in another collection · chain A 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 Q5CYZ2
- Elsewhere: RCSB PDB 4ND3 · PDBe 4ND3 · UniProt Q5CYZ2
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