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Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) complexed with a lipophilic phosphonate inhibitor
Analyse Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RAS
- Type
- protein
- Length
- 758 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- EC
- 1.1.1.267
- UniProt
- P64012
- Ligands
- NDP, FM5, DCV, MN, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 379 | 47% helix, 16% strand | P64012 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FM5 · 3-(N-hydroxyacetamido)-1-(3,4-dichlorophenyl)propylphosphonic acid · ligand · 2 copies · chains A, B
- DCV · [(1R)-3-[acetyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.77 | 0.83 | 93 | NDP, FM5, DCV, MN |
| 2 | 710 | 0.70 | 0.77 | 78 | NDP, MN, SO4 |
| 3 | 100 | 0.42 | 0.77 | 21 | empty |
| 4 | 103 | 0.40 | 0.76 | 16 | empty |
| 5 | 88 | 0.37 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1730 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3RAS · Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with… · 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 P64012
- Elsewhere: RCSB PDB 3RAS · PDBe 3RAS · UniProt P64012
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