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Structure of plasmodium falciparum dxr in complex with a beta- substituted fosmidomycin analogue, RC137, 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
- 4Y6R
- 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, apicoplast
- EC
- 1.1.1.267
- UniProt
- Q8IKG4
- Ligands
- RF7, MN, CL, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast (EC 1.1.1.267) | protein | 410 | 51% helix, 15% strand | Q8IKG4 |
Ligands and binding sites
- RF7 · {(2R)-4-[hydroxy(methyl)amino]-4-oxo-2-phenylbutyl}phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.76 | 0.98 | 28 | empty |
| 2 | 369 | 0.75 | 0.86 | 66 | RF7 |
| 3 | 353 | 0.72 | 0.84 | 56 | RF7, CL |
| 4 | 84 | 0.51 | 0.84 | 14 | empty |
| 5 | 63 | 0.43 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1975 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4Y6R · 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 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 Q8IKG4
- Elsewhere: RCSB PDB 4Y6R · PDBe 4Y6R · UniProt Q8IKG4
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