MolNFT v1 · #13500 · protein
Refined crystal structure of dogfish M4 apo-lactate dehydrogenase
1LDM · M4 lactate dehydrogenase: “Refined crystal structure of dogfish M4 apo-lactate dehydrogenase”. X-ray diffraction, 2 ligands (OXM, NAD), 2 pockets (best druggability 0.72). MolNFT v1 #13500 on GenesisL1: 3D structure, binding sites…
- PDB
- 1LDM
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M4 lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00341
- Ligands
- OXM, NAD
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M4 lactate dehydrogenase (EC 1.1.1.27) | protein | 329 | 45% helix, 17% strand | P00341 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 2 copies · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.72 | 0.87 | 40 | NAD, OXM |
| 2 | 155 | 0.42 | 0.74 | 24 | empty |
Compared structures
- 1LDM · Refined crystal structure of dogfish M4 apo-lactate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P00341 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P00341) · 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 P00341
- Elsewhere: RCSB PDB 1LDM · PDBe 1LDM · UniProt P00341
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.