Research workbench
Crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme.
Analyse Crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F0X
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-lactate dehydrogenase
- EC
- 1.1.1.28
- UniProt
- P06149
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-lactate dehydrogenase (EC 1.1.1.28) | protein | 502 | 34% helix, 22% strand | P06149 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.83 | 0.92 | 55 | FAD |
| 2 | 348 | 0.82 | 0.92 | 57 | FAD |
| 3 | 270 | 0.59 | 0.79 | 35 | empty |
| 4 | 344 | 0.57 | 0.76 | 39 | empty |
| 5 | 256 | 0.56 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 263 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1F0X · Crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. · the same entry in another collection · chain A against A, TM-score 1.00
- P06149 · AlphaFold monomer V2.0 prediction for quinone-dependent D-lactate dehydrogenase (P06149) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P06149
- Elsewhere: RCSB PDB 1F0X · PDBe 1F0X · UniProt P06149
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