Research workbench
Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC56 and manganese
Analyse Structure of Plasmodium falciparum DXR in complex with a beta-substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JO0
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Plasmodium falciparum 3D7
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
- EC
- 1.1.1.267
- UniProt
- Q8IKG4
- Ligands
- L56, 6LR, MN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic (EC 1.1.1.267) | protein | 410 | 52% helix, 15% strand | Q8IKG4 |
Ligands and binding sites
- L56 · [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methylphenyl)pentyl]phosphonic acid · ligand · 2 copies · chains A, B
- 6LR · morpholine · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.76 | 0.83 | 66 | L56, GOL |
| 2 | 615 | 0.75 | 0.82 | 62 | L56, MN, GOL |
| 3 | 72 | 0.74 | 0.98 | 28 | empty |
| 4 | 84 | 0.51 | 0.83 | 17 | EDO |
| 5 | 74 | 0.44 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1991 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5JO0 · Structure of plasmodium falciparum dxr in complex with a beta- substituted fosmidomycin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IKG4 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8IKG4
- Elsewhere: RCSB PDB 5JO0 · PDBe 5JO0 · UniProt Q8IKG4
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