Research workbench
Design and synthesis of new enzymes based on the lactate dehydrogenase framework
Analyse Design and synthesis of new enzymes based on the lactate dehydrogenase framework in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9LDT
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00339
- Ligands
- ACE, NAD, OXM, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactate dehydrogenase (EC 1.1.1.27) | protein | 331 | 45% helix, 18% strand | P00339 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- OXM · Oxamic acid · ligand · 2 copies · chains A, B
- 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.73 | 0.91 | 32 | NAD, OXM |
| 2 | 263 | 0.72 | 0.86 | 42 | NAD, OXM |
| 3 | 113 | 0.51 | 0.82 | 24 | empty |
| 4 | 125 | 0.50 | 0.80 | 25 | empty |
| 5 | 121 | 0.49 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2926 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 9LDT · Design and synthesis of new enzymes based on the lactate dehydrogenase framework · the same entry in another collection · chain A against A, TM-score 1.00
- P00339 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P00339) · 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 P00339
- Elsewhere: RCSB PDB 9LDT · PDBe 9LDT · UniProt P00339
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