MolNFT v1 · #100964 · protein
Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor analog (3-acetylpyridine adenine dinucleotide)
4ND2 · Lactate dehydrogenase, adjacent gene encodes predicted…: “Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic…”. X-ray diffraction, 2 ligands (A3D, PYR), 10 pockets (best…
- PDB
- 4ND2
- 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
- A3D, PYR
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% 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 | 50% helix, 20% strand | Q5CYZ2 |
Ligands and binding sites
- A3D · 3-acetylpyridine adenine dinucleotide · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · 2 copies · chains A, 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.70 | 0.83 | 50 | A3D, PYR |
| 2 | 341 | 0.69 | 0.82 | 44 | A3D, PYR |
| 3 | 65 | 0.63 | 0.92 | 19 | empty |
| 4 | 130 | 0.50 | 0.80 | 24 | empty |
| 5 | 104 | 0.49 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2078 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4ND2 · 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 4ND2 · PDBe 4ND2 · UniProt Q5CYZ2
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