Research workbench
2.5 ångström resolution crystal structure of dihydrolipoyl dehydrogenase from pseudomonas putida in complex with FAD.
Analyse 2.5 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
- 5TR3
- Type
- protein
- Length
- 948 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
- FAD
- Pockets
- 11 · best druggability 0.85
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 | 474 | 33% helix, 27% strand | Q88FB1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.85 | 0.86 | 75 | empty |
| 2 | 822 | 0.79 | 0.82 | 77 | FAD |
| 3 | 763 | 0.78 | 0.82 | 77 | FAD |
| 4 | 201 | 0.76 | 0.91 | 37 | empty |
| 5 | 59 | 0.69 | 0.96 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3597 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 5TR3 · 2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas… · 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 5TR3 · PDBe 5TR3 · UniProt Q88FB1
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