Research workbench
Crystal structure of dox-P reductoisomerase fosmidomycin and magnesium
Analyse Crystal structure of dox-P reductoisomerase fosmidomycin and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZQF
- Type
- protein
- Length
- 804 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
- A0A076U3E6
- Ligands
- FOM, MG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 402 | 53% helix, 15% strand | A0A076U3E6 |
Ligands and binding sites
- FOM · 3-[formyl(hydroxy)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.71 | 0.85 | 32 | empty |
| 2 | 645 | 0.70 | 0.78 | 77 | FOM |
| 3 | 575 | 0.68 | 0.78 | 74 | FOM |
| 4 | 103 | 0.56 | 0.84 | 18 | empty |
| 5 | 90 | 0.56 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1799 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4ZQF · Crystal structure of DOX-P Reductoisomerase fosmidomycin and magnesium · 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 A0A076U3E6
- Elsewhere: RCSB PDB 4ZQF · PDBe 4ZQF · UniProt A0A076U3E6
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