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
- 1J4A
- Type
- protein
- Length
- 1,325 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- P26297
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 331 | 40% helix, 17% strand | P26297 |
| D | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 332 | 40% helix, 17% strand | P26297 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.72 | 0.77 | 86 | SO4 |
| 2 | 548 | 0.67 | 0.77 | 52 | SO4 |
| 3 | 503 | 0.65 | 0.77 | 50 | SO4 |
| 4 | 468 | 0.64 | 0.77 | 56 | SO4 |
| 5 | 179 | 0.59 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2958 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 2948 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1J4A · 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 0.99
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 1J4A · PDBe 1J4A · UniProt P26297
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