MolNFT v1 · #11746 · protein
Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase; a target enzyme for antimalarial drugs
1JVS: “Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase; a target enzyme for antimalarial drugs”. X-ray diffraction, 2 ligands (NDP, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #11746 on GenesisL1: 3D structure…
- PDB
- 1JVS
- Type
- protein
- Length
- 798 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
- P45568
- Ligands
- NDP, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 400 | 50% helix, 15% strand | P45568 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 398 | 52% helix, 15% strand | P45568 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.76 | 0.90 | 37 | empty |
| 2 | 463 | 0.71 | 0.81 | 60 | SO4, NDP |
| 3 | 476 | 0.71 | 0.81 | 56 | SO4, NDP |
| 4 | 66 | 0.33 | 0.76 | 19 | empty |
| 5 | 55 | 0.31 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1627 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1JVS · Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase; a target enzyme for… · the same entry in another collection · chain A against A, TM-score 1.00
- P45568 · 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 0.96
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 P45568
- Elsewhere: RCSB PDB 1JVS · PDBe 1JVS · UniProt P45568
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