Research workbench
Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa bound to NADH
Analyse Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa bound to NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U8W
- Type
- protein
- Length
- 1,891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- A0A0H2Z9F5
- Ligands
- FAD, NAI
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 473 | 33% helix, 28% strand | A0A0H2Z9F5 |
| D | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 472 | 33% helix, 28% strand | A0A0H2Z9F5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.86 | 0.91 | 50 | empty |
| 2 | 773 | 0.85 | 0.88 | 62 | DMS |
| 3 | 863 | 0.79 | 0.81 | 96 | FAD, NAI, DMS |
| 4 | 841 | 0.79 | 0.82 | 94 | FAD, NAI, DMS |
| 5 | 846 | 0.78 | 0.81 | 105 | FAD, NAI, DMS |
Interfaces
4 interfaces between chains.
- A–B · 3577 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3560 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5U8W · Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH · 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 A0A0H2Z9F5
- Elsewhere: RCSB PDB 5U8W · PDBe 5U8W · UniProt A0A0H2Z9F5
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