MolNFT v1 · #124695 · protein
The structure of G164E variant of type II NADH dehydrogenase from caldalkalibacillus thermarum
5KMP · FAD-dependent pyridine nucleotide-disulfide oxidoreductase: “The structure of G164E variant of type II NADH dehydrogenase from caldalkalibacillus thermarum”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.81).…
- 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
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