Research workbench
Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4.
Analyse Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VDJ
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- Ligands
- TXD, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase | protein | 308 | 51% helix, 20% strand | — |
| B | Lactate dehydrogenase | protein | 317 | 51% helix, 20% strand | — |
Ligands and binding sites
- TXD · 1,4,5,6-tetrahydronicotinamide adenine dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.73 | 0.80 | 70 | SO4 |
| 2 | 459 | 0.64 | 0.77 | 63 | TXD, SO4 |
| 3 | 259 | 0.61 | 0.80 | 46 | empty |
| 4 | 149 | 0.53 | 0.80 | 20 | empty |
| 5 | 70 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2079 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6VDJ · Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4. · 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 6VDJ · PDBe 6VDJ
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