MolNFT v1 · #13501 · protein
Structure of a ternary complex of an allosteric lactate dehydrogenase from bacillus stearothermophilus at 2.5 ångströms resolution
1LDN · L-lactate dehydrogenase: “Structure of a ternary complex of an allosteric lactate dehydrogenase from bacillus stearothermophilus at 2.5…”. X-ray diffraction, 3 ligands (OXM, NAD, FBP), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 1LDN
- Type
- protein
- Length
- 2,528 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00344
- Ligands
- OXM, NAD, FBP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 316 | 46% helix, 22% strand | P00344 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.83 | 0.92 | 49 | FBP |
| 2 | 280 | 0.81 | 0.93 | 43 | FBP |
| 3 | 285 | 0.81 | 0.92 | 48 | FBP |
| 4 | 270 | 0.80 | 0.92 | 45 | FBP |
| 5 | 184 | 0.73 | 0.90 | 29 | OXM, NAD |
Interfaces
13 interfaces between chains.
- A–D · 2137 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2136 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 2118 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 2108 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 984 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1LDN · Structure of a ternary complex of an allosteric lactate dehydrogenase from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P00344 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P00344) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00344
- Elsewhere: RCSB PDB 1LDN · PDBe 1LDN · UniProt P00344
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