Research workbench
1.83 ångström resolution crystal structure of dihydrolipoyl dehydrogenase from pseudomonas putida in complex with FAD and adenosine-5'-monophosphate.
Analyse 1.83 ångström resolution crystal structure of dihydrolipoyl dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AWA
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- Q88FB1
- Ligands
- AMP, FAD, SO4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 475 | 33% helix, 27% strand | Q88FB1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.84 | 0.86 | 77 | empty |
| 2 | 827 | 0.80 | 0.82 | 80 | FAD |
| 3 | 897 | 0.79 | 0.82 | 97 | AMP, FAD |
| 4 | 377 | 0.76 | 0.86 | 57 | empty |
| 5 | 400 | 0.74 | 0.84 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 3588 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6AWA · 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from… · 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
- Every structure of UniProt Q88FB1
- Elsewhere: RCSB PDB 6AWA · PDBe 6AWA · UniProt Q88FB1
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