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The structure of type II NADH dehydrogenase from caldalkalibacillus thermarum complexed with NAD+ at 2.5 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
- 5KMS
- Type
- protein
- Length
- 1,578 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
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 37% helix, 28% strand | F5L3B8 |
| B, D | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 395 | 37% helix, 27% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.85 | 0.86 | 116 | FAD |
| 2 | 1055 | 0.81 | 0.82 | 104 | FAD |
| 3 | 960 | 0.81 | 0.82 | 86 | FAD, NAD |
| 4 | 921 | 0.80 | 0.82 | 85 | FAD |
| 5 | 192 | 0.56 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 891 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 886 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KMS · The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed… · 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 5KMS · PDBe 5KMS · UniProt F5L3B8
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