Research workbench
Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a qui inhibitor HQNO at 2.8A resolution
Analyse Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BDO
- Type
- protein
- Length
- 1,577 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Caldalkalibacillus thermarum TA2.A1
- Molecule
- FAD-dependent pyridine nucleotide-disulfide oxidoreductase
- UniProt
- F5L3B8
- Ligands
- FAD, HQO
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 37% helix, 28% strand | F5L3B8 |
| D | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 395 | 36% helix, 28% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains B, A, D, C
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.81 | 0.84 | 81 | FAD |
| 2 | 1042 | 0.81 | 0.82 | 91 | FAD |
| 3 | 1109 | 0.80 | 0.82 | 107 | FAD, HQO |
| 4 | 1112 | 0.80 | 0.81 | 91 | FAD, HQO |
| 5 | 96 | 0.54 | 0.84 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–A · 893 Ų buried · 26 hydrogen bonds · protein-protein
- D–C · 881 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BDO · Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus thermarum… · 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 F5L3B8
- Elsewhere: RCSB PDB 6BDO · PDBe 6BDO · UniProt F5L3B8
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