MolNFT v1 · #135172 · protein
2.5 ångström resolution crystal structure of dihydrolipoyl dehydrogenase from pseudomonas putida in complex with FAD.
5TR3: “2.5 ångström resolution crystal structure of dihydrolipoyl dehydrogenase from pseudomonas putida in complex…”. X-ray diffraction, 1 ligand (FAD), 11 pockets (best druggability 0.85). MolNFT v1 #135172 on GenesisL1: 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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