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The structure of type II NADH dehydrogenase from caldalkalibacillus thermarum complexed with NAD+ at 3.0 ångström resolution.
Analyse The structure of type II NADH dehydrogenase from caldalkalibacillus thermarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KMR
- Type
- protein
- Length
- 1,572 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, NAD
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 37% helix, 27% strand | F5L3B8 |
| A | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 393 | 37% helix, 27% strand | F5L3B8 |
| C | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 391 | 38% helix, 27% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains B, A, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.82 | 0.83 | 90 | FAD |
| 2 | 891 | 0.81 | 0.83 | 92 | FAD, NAD |
| 3 | 1046 | 0.81 | 0.82 | 108 | FAD, NAD |
| 4 | 917 | 0.80 | 0.82 | 73 | FAD, NAD |
| 5 | 271 | 0.60 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–A · 889 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 885 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5KMR · The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed… · 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 5KMR · PDBe 5KMR · UniProt F5L3B8
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