Research workbench
The structure of G164E variant of type II NADH dehydrogenase from caldalkalibacillus thermarum
Analyse The structure of G164E variant of type II NADH dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KMP
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent pyridine nucleotide-disulfide oxidoreductase
- UniProt
- F5L3B8
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 37% helix, 26% strand | F5L3B8 |
| B | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 395 | 36% helix, 26% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.81 | 0.82 | 78 | FAD |
| 2 | 1061 | 0.80 | 0.81 | 92 | FAD |
| 3 | 126 | 0.53 | 0.81 | 24 | empty |
| 4 | 156 | 0.52 | 0.79 | 24 | empty |
| 5 | 143 | 0.38 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5KMP · The structure of G164E variant of type II NADH dehydrogenase from Caldalkalibacillus… · 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 5KMP · PDBe 5KMP · UniProt F5L3B8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.