Research workbench
Crystal structure of ancestral apicomplexan lactate dehydrogenase with oxamate.
Analyse Crystal structure of ancestral apicomplexan lactate dehydrogenase with oxamate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLG
- Type
- protein
- Length
- 645 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- Ligands
- OXM, NAI, NA
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase | protein | 324 | 49% helix, 19% strand | — |
| B | Lactate dehydrogenase | protein | 321 | 50% helix, 20% strand | — |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 8 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.69 | 0.86 | 42 | OXM, NAI |
| 2 | 202 | 0.67 | 0.85 | 41 | OXM, NA, NAI |
| 3 | 79 | 0.54 | 0.86 | 21 | empty |
| 4 | 94 | 0.52 | 0.84 | 24 | empty |
| 5 | 87 | 0.46 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4PLG · Crystal structure of ancestral apicomplexan lactate dehydrogenase with oxamate. · 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 4PLG · PDBe 4PLG
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