MolNFT v1 · #177664 · protein
Human ldhc complexed with NAD+ and ethylamino acetic acid
7EPM · L-lactate dehydrogenase C chain: “Human ldhc complexed with NAD+ and ethylamino acetic acid”. X-ray diffraction, 3 ligands (J9X, NAD, SO4), 8 pockets (best druggability 0.74). MolNFT v1 #177664 on GenesisL1: 3D structure, binding…
- PDB
- 7EPM
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase C chain
- EC
- 1.1.1.27
- UniProt
- P07864
- Ligands
- J9X, NAD, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase C chain (EC 1.1.1.27) | protein | 335 | 44% helix, 17% strand | P07864 |
| B | L-lactate dehydrogenase C chain (EC 1.1.1.27) | protein | 326 | 44% helix, 18% strand | P07864 |
Ligands and binding sites
- J9X · 2-(ethylamino)-2-oxidanylidene-ethanoic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.74 | 0.87 | 39 | J9X, NAD |
| 2 | 297 | 0.73 | 0.86 | 45 | J9X, NAD |
| 3 | 641 | 0.70 | 0.78 | 79 | SO4 |
| 4 | 145 | 0.49 | 0.78 | 32 | empty |
| 5 | 104 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7EPM · human LDHC complexed with NAD+ and ethylamino acetic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P07864 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase C chain (P07864) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P07864
- Elsewhere: RCSB PDB 7EPM · PDBe 7EPM · UniProt P07864
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