MolNFT v1 · #110040 · protein
A novel D-lactate dehydrogenase from sporolactobacillus sp
4XKJ: “A novel D-lactate dehydrogenase from sporolactobacillus sp”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.73). MolNFT v1 #110040 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XKJ
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-lactate dehydrogenase | protein | 332 | 39% helix, 15% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.73 | 0.79 | 68 | NAD |
| 2 | 653 | 0.65 | 0.75 | 53 | NAD |
| 3 | 390 | 0.63 | 0.78 | 50 | empty |
| 4 | 117 | 0.41 | 0.76 | 19 | empty |
| 5 | 76 | 0.37 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2808 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 4XKJ · a Novel D-lactate Dehydrogenase from Sporolactobacillus sp · 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
- Elsewhere: RCSB PDB 4XKJ · PDBe 4XKJ
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