Research workbench
Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 ångströms resolution
Analyse Structure of the active ternary complex of pig heart lactate dehydrogenase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LDH
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P00336
- Ligands
- ACE, LNC
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactate dehydrogenase (EC 1.1.1.27) | protein | 333 | 39% helix, 10% strand | P00336 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- LNC · (3S)-5-(3-carboxy-3-hydroxypropyl) nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.81 | 0.91 | 73 | empty |
| 2 | 268 | 0.78 | 0.90 | 40 | LNC |
| 3 | 592 | 0.76 | 0.82 | 89 | LNC |
| 4 | 232 | 0.70 | 0.86 | 29 | empty |
| 5 | 199 | 0.69 | 0.87 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2084 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5LDH · Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD… · the same entry in another collection · chain A against A, TM-score 1.00
- P00336 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase B chain (P00336) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P00336
- Elsewhere: RCSB PDB 5LDH · PDBe 5LDH · UniProt P00336
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