MolNFT v1 · #135767 · protein
Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa bound to NAD+
5U8V · Dihydrolipoyl dehydrogenase: “Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa bound to NAD+”. X-ray diffraction, 2 ligands (FAD, NAD), 16 pockets (best druggability 0.86). MolNFT v1 #135767 on GenesisL1: 3D…
- PDB
- 5U8V
- Type
- protein
- Length
- 1,894 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, NAD
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 472 | 33% helix, 28% strand | A0A0H2Z9F5 |
| B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 473 | 33% helix, 28% strand | A0A0H2Z9F5 |
| C | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 474 | 34% helix, 29% strand | A0A0H2Z9F5 |
| D | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 475 | 33% helix, 29% strand | A0A0H2Z9F5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 32 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.86 | 0.90 | 55 | empty |
| 2 | 844 | 0.86 | 0.88 | 73 | DMS |
| 3 | 815 | 0.79 | 0.82 | 94 | FAD, NAD, DMS |
| 4 | 762 | 0.79 | 0.83 | 87 | FAD, NAD, DMS |
| 5 | 877 | 0.79 | 0.81 | 95 | FAD, NAD, DMS |
Interfaces
5 interfaces between chains.
- A–B · 3547 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3540 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5U8V · Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NAD+ · 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 5U8V · PDBe 5U8V · UniProt A0A0H2Z9F5
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