Research workbench
Crystal structure of ancestral apicomplexan lactate dehydrogenase with malate.
Analyse Crystal structure of ancestral apicomplexan lactate dehydrogenase with malate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLC
- Type
- protein
- Length
- 1,296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- Ligands
- PYR, NAI, NAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lactate dehydrogenase | protein | 324 | 51% helix, 19% strand | — |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, C
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.84 | 0.85 | 111 | empty |
| 2 | 673 | 0.78 | 0.83 | 88 | PYR, NAI, NAD |
| 3 | 614 | 0.76 | 0.82 | 80 | PYR, NAD, NAI |
| 4 | 56 | 0.69 | 0.98 | 21 | empty |
| 5 | 54 | 0.68 | 0.97 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2130 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2093 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1556 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1540 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 892 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4PLC · Crystal structure of ancestral apicomplexan lactate dehydrogenase with malate. · 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 4PLC · PDBe 4PLC
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