Research workbench
Insights into domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from lactobacillus bulgaricus
Analyse Insights into domain closure, substrate specificity and catalysis of D-lactate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J49
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- P26297
- Ligands
- NAD, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 332 | 39% helix, 17% strand | P26297 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.69 | 0.82 | 47 | SO4, NAD |
| 2 | 581 | 0.67 | 0.77 | 50 | NAD |
| 3 | 147 | 0.57 | 0.82 | 23 | empty |
| 4 | 127 | 0.47 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2886 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 1J49 · Insights into domain closure, substrate specificity and catalysis of D-lactate… · the same entry in another collection · chain A against A, TM-score 1.00
- P26297 · AlphaFold monomer V2.0 prediction for D-lactate dehydrogenase (P26297) · a predicted model of the same protein · 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
- Every structure of UniProt P26297
- Elsewhere: RCSB PDB 1J49 · PDBe 1J49 · UniProt P26297
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