Research workbench
X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in the presence of lactate or phenyl-lactate
Analyse X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LDC
- Type
- protein
- Length
- 860 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, PYR, HEM
- Pockets
- 11 · best druggability 0.85
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 | 478 | 41% helix, 12% strand | P00175 |
| B | L-lactate dehydrogenase (EC 1.1.2.3) | protein | 382 | 43% helix, 13% strand | P00175 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PYR · Pyruvic 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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.85 | 0.86 | 117 | FMN, HEM, PYR |
| 2 | 270 | 0.71 | 0.86 | 46 | FMN, PYR |
| 3 | 118 | 0.47 | 0.79 | 23 | empty |
| 4 | 62 | 0.42 | 0.81 | 13 | empty |
| 5 | 71 | 0.41 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2507 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1LDC · 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 1LDC · PDBe 1LDC · UniProt P00175
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