Research workbench
Structure of NDH2 from plasmodium falciparum in complex with NADH
Analyse Structure of NDH2 from plasmodium falciparum in complex with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JWB
- Type
- protein
- Length
- 985 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II NADH:UBIQUINONE oxidoreductase
- EC
- 1.6.5.3
- UniProt
- Q8I302
- Ligands
- TRT, FAD, NAD, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II NADH:UBIQUINONE oxidoreductase (EC 1.6.5.3) | protein | 493 | 38% helix, 22% strand | Q8I302 |
| H | Type II NADH:UBIQUINONE oxidoreductase (EC 1.6.5.3) | protein | 492 | 39% helix, 22% strand | Q8I302 |
Ligands and binding sites
- TRT · Fragment of triton X-100 · ligand · 6 copies · chains A, H
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, H
- MG · Magnesium ion · metal · 8 copies · chains A, H
- ACT · Acetate ion · additive · 7 copies · chains A, H
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 2 copies · chains A, H
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 | 909 | 0.79 | 0.81 | 83 | FAD, MG, NAD |
| 2 | 1175 | 0.77 | 0.79 | 102 | FAD, MG, NAD |
| 3 | 607 | 0.77 | 0.83 | 43 | ACT |
| 4 | 254 | 0.63 | 0.81 | 30 | TRT, CXS |
| 5 | 232 | 0.61 | 0.80 | 24 | TRT, CXS |
Interfaces
1 interface between chains.
- A–H · 2025 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5JWB · Structure of NDH2 from plasmodium falciparum in complex with NADH · 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 Q8I302
- Elsewhere: RCSB PDB 5JWB · PDBe 5JWB · UniProt Q8I302
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