MolNFT v1 · #16886 · protein
Lactate dehydrogenase from plasmodium berghei
1OC4 · L-lactate dehydrogenase: “Lactate dehydrogenase from plasmodium berghei”. X-ray diffraction, 2 ligands (NAD, OXM), 8 pockets (best druggability 0.71). MolNFT v1 #16886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OC4
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q4Z783
- Ligands
- NAD, OXM
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 49% helix, 20% strand | Q4Z783 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- OXM · Oxamic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.71 | 0.83 | 58 | GOL |
| 2 | 234 | 0.69 | 0.85 | 36 | NAD, OXM |
| 3 | 231 | 0.69 | 0.85 | 39 | NAD, OXM |
| 4 | 63 | 0.58 | 0.90 | 22 | empty |
| 5 | 103 | 0.41 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1OC4 · Lactate dehydrogenase from Plasmodium berghei · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4Z783
- Elsewhere: RCSB PDB 1OC4 · PDBe 1OC4 · UniProt Q4Z783
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