MolNFT v1 · #156850 · protein
Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from staphylococcus schleiferi in complex with fosmidomycin (fom)
6MH5 · 1-deoxy-D-xylulose 5-phosphate reductoisomerase: “Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from staphylococcus schleiferi in…”. X-ray diffraction, 1 ligand (FOM), 12 pockets (best druggability 0.80).…
- PDB
- 6MH5
- Type
- protein
- Length
- 749 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
- A0A0K1A7V6
- Ligands
- FOM
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | 374 | 46% helix, 15% strand | A0A0K1A7V6 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 375 | 47% helix, 15% strand | A0A0K1A7V6 |
Ligands and binding sites
- FOM · 3-[formyl(hydroxy)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.80 | 0.95 | 39 | FOM |
| 2 | 593 | 0.74 | 0.81 | 75 | FOM |
| 3 | 341 | 0.69 | 0.82 | 29 | empty |
| 4 | 371 | 0.67 | 0.81 | 56 | empty |
| 5 | 100 | 0.40 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MH5 · Crystal Structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Staphylococcus… · 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 A0A0K1A7V6
- Elsewhere: RCSB PDB 6MH5 · PDBe 6MH5 · UniProt A0A0K1A7V6
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