Research workbench
Crystal structure of lactate dehydrogenase from selenomonas ruminantium with NADH.
Analyse Crystal structure of lactate dehydrogenase from selenomonas ruminantium with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NAY
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q9EVR0
- Ligands
- NAD, BO3
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 322 | 46% helix, 22% strand | Q9EVR0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- BO3 · Boric acid · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- MLA · Malonic acid · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.65 | 0.83 | 38 | NAD, MLA, EDO |
| 2 | 95 | 0.33 | 0.73 | 20 | empty |
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7NAY · Crystal structure of lactate dehydrogenase from Selenomonas ruminantium with NADH. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EVR0 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (Q9EVR0) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9EVR0
- Elsewhere: RCSB PDB 7NAY · PDBe 7NAY · UniProt Q9EVR0
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