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Structure of plasmodium falciparum dxr in complex with a beta- substituted fosmidomycin analogue, LC51 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
- 5JAZ
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
- EC
- 1.1.1.267
- UniProt
- Q8IKG4
- Ligands
- LC5, MN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 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
- LC5 · [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(naphthalen-1-yl)pentyl]phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.77 | 0.98 | 28 | FMT |
| 2 | 588 | 0.75 | 0.82 | 67 | LC5, MN, GOL |
| 3 | 582 | 0.74 | 0.82 | 74 | LC5, GOL |
| 4 | 80 | 0.45 | 0.80 | 19 | empty |
| 5 | 70 | 0.43 | 0.81 | 21 | FMT |
Interfaces
1 interface between chains.
- A–B · 1948 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5JAZ · 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 5JAZ · PDBe 5JAZ · UniProt Q8IKG4
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