MolNFT v1 · #13472 · protein
X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in the presence of lactate or phenyl-lactate
1LCO · L-lactate dehydrogenase: “X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in the presence of…”. X-ray diffraction, 3 ligands (FMN, PPY, HEM), 12 pockets (best druggability 0.86). MolNFT v1 #13472…
- PDB
- 1LCO
- Type
- protein
- Length
- 871 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.2.3
- UniProt
- P00175
- Ligands
- FMN, PPY, HEM
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.2.3) | protein | 480 | 41% helix, 14% strand | P00175 |
| B | L-lactate dehydrogenase (EC 1.1.2.3) | protein | 391 | 43% helix, 13% strand | P00175 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PPY · 3-phenylpyruvic acid · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.86 | 0.88 | 94 | HEM, FMN, PPY |
| 2 | 615 | 0.77 | 0.83 | 70 | FMN, PPY |
| 3 | 218 | 0.54 | 0.77 | 30 | empty |
| 4 | 110 | 0.46 | 0.79 | 21 | empty |
| 5 | 58 | 0.43 | 0.82 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2645 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1LCO · X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00175 · AlphaFold monomer V2.0 prediction for cytochrome B2, mitochondrial (P00175) · 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 P00175
- Elsewhere: RCSB PDB 1LCO · PDBe 1LCO · UniProt P00175
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