Research workbench
Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus thermarum at 2.15A 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
- 5WED
- Type
- protein
- Length
- 1,576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent pyridine nucleotide-disulfide oxidoreductase
- UniProt
- F5L3B8
- Ligands
- FAD
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 36% helix, 28% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.83 | 0.84 | 107 | FAD |
| 2 | 1063 | 0.81 | 0.82 | 102 | FAD |
| 3 | 1012 | 0.81 | 0.82 | 96 | FAD |
| 4 | 1156 | 0.80 | 0.81 | 103 | FAD |
| 5 | 114 | 0.52 | 0.82 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 897 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 888 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WED · Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at… · the same entry in another collection · chain B against B, 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 5WED · PDBe 5WED · UniProt F5L3B8
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