Research workbench
Dictyostelium discoideum lactate dehydrogenase (dicldha)
Analyse Dictyostelium discoideum lactate dehydrogenase (dicldha) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WN9
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- Q54UF7
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative D-lactate dehydrogenase (EC 1.1.1.28) | protein | 339 | 40% helix, 17% strand | Q54UF7 |
| B | Putative D-lactate dehydrogenase (EC 1.1.1.28) | protein | 341 | 40% helix, 17% strand | Q54UF7 |
Ligands and binding sites
- ACT · Acetate ion · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.66 | 0.79 | 46 | ACT |
| 2 | 330 | 0.66 | 0.81 | 44 | ACT |
| 3 | 136 | 0.43 | 0.76 | 25 | empty |
| 4 | 106 | 0.41 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2848 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7WN9 · Dictyostelium discoideum Lactate dehydrogenase (DicLDHA) · the same entry in another collection · chain A against A, TM-score 1.00
- Q54UF7 · AlphaFold monomer V2.0 prediction for putative D-lactate dehydrogenase (Q54UF7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q54UF7
- Elsewhere: RCSB PDB 7WN9 · PDBe 7WN9 · UniProt Q54UF7
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