MolNFT v1 · #145400 · protein
2.3 ångström resolution crystal structure of dihydrolipoamide dehydrogenase from burkholderia cenocepacia in complex with FAD and NAD
6CMZ · Dihydrolipoyl dehydrogenase: “2.3 ångström resolution crystal structure of dihydrolipoamide dehydrogenase from burkholderia cenocepacia in…”. X-ray diffraction, 6 ligands (FAD, ADP, NAD), 18 pockets (best druggability 0.87). MolNFT…
- PDB
- 6CMZ
- Type
- protein
- Length
- 1,842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- B4EEF2
- Ligands
- FAD, ADP, NAD, FMN, MLT, CL
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 462 | 34% helix, 27% strand | B4EEF2 |
| B, D | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 459 | 35% helix, 27% strand | B4EEF2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 5 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- MLT · D-malate · ligand · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C
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 | 1075 | 0.87 | 0.88 | 135 | FAD |
| 2 | 813 | 0.86 | 0.88 | 64 | empty |
| 3 | 762 | 0.85 | 0.89 | 77 | MLT |
| 4 | 404 | 0.80 | 0.89 | 70 | FAD |
| 5 | 702 | 0.80 | 0.84 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3417 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3380 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6CMZ · 2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide 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 B4EEF2
- Elsewhere: RCSB PDB 6CMZ · PDBe 6CMZ · UniProt B4EEF2
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