Research workbench
Structure of NDH2 from plasmodium falciparum in complex with ryl-552
Analyse Structure of NDH2 from plasmodium falciparum in complex with ryl-552 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JWC
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH dehydrogenase, putative
- EC
- 1.6.99.3
- UniProt
- Q8I302
- Ligands
- TRT, 4W0, FAD, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | NADH dehydrogenase, putative (EC 1.6.99.3) | protein | 495 | 38% helix, 23% strand | Q8I302 |
Ligands and binding sites
- TRT · Fragment of triton X-100 · ligand · 6 copies · chains A, H
- 4W0 · 5-fluoro-3-methyl-2-{4-[4-(trifluoromethoxy)benzyl]phenyl}quinolin-4(1H)-one · ligand · 4 copies · chains A, H
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, H
- MG · Magnesium ion · metal · 8 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.79 | 0.81 | 77 | FAD, MG, TRT |
| 2 | 705 | 0.77 | 0.82 | 45 | 4W0 |
| 3 | 1098 | 0.77 | 0.79 | 87 | FAD, MG, TRT |
| 4 | 244 | 0.61 | 0.80 | 28 | 4W0 |
| 5 | 195 | 0.60 | 0.81 | 21 | 4W0 |
Interfaces
1 interface between chains.
- A–H · 1851 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5JWC · Structure of NDH2 from plasmodium falciparum in complex with RYL-552 · 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 5JWC · PDBe 5JWC · UniProt Q8I302
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