MolNFT v1 · #191584 · protein
Design and synthesis of new enzymes based on the lactate dehydrogenase framework
9LDT: “Design and synthesis of new enzymes based on the lactate dehydrogenase framework”. X-ray diffraction, 4 ligands (ACE, NAD, OXM), 7 pockets (best druggability 0.73). MolNFT v1 #191584 on GenesisL1: 3D structure, binding sites and…
- 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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