MolNFT v1 · #103596 · protein
Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.
4PLF: “Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate.”. X-ray diffraction, 3 ligands (PYR, NAI, NAD), 10 pockets (best druggability 0.69). MolNFT v1 #103596 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PLF
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- Ligands
- PYR, NAI, NAD
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase | protein | 325 | 49% helix, 19% strand | — |
| B | Lactate dehydrogenase | protein | 330 | 49% helix, 19% strand | — |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.69 | 0.86 | 42 | NAD, PYR |
| 2 | 207 | 0.68 | 0.85 | 41 | NAI, PYR |
| 3 | 56 | 0.57 | 0.91 | 17 | empty |
| 4 | 79 | 0.54 | 0.86 | 23 | empty |
| 5 | 97 | 0.46 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1473 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4PLF · Crystal structure of ancestral apicomplexan lactate dehydrogenase with lactate. · 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
- Elsewhere: RCSB PDB 4PLF · PDBe 4PLF
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