MolNFT v1 · #57195 · protein
Crystal structure of dxr from thermooga maritia, in complex with fosmidomycin and NADPH
3A06 · 1-deoxy-D-xylulose 5-phosphate reductoisomerase: “Crystal structure of dxr from thermooga maritia, in complex with fosmidomycin and NADPH”. X-ray diffraction, 3 ligands (NDP, FOM, MG), 7 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 3A06
- Type
- protein
- Length
- 743 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
- Q9WZZ1
- Ligands
- NDP, FOM, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 370 | 46% helix, 16% strand | Q9WZZ1 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 373 | 47% helix, 16% strand | Q9WZZ1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B
- 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.75 | 0.83 | 71 | NDP, FOM, MG |
| 2 | 498 | 0.74 | 0.83 | 71 | NDP, FOM, MG |
| 3 | 85 | 0.40 | 0.77 | 14 | empty |
| 4 | 77 | 0.37 | 0.76 | 15 | empty |
| 5 | 67 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1924 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3A06 · Crystal structure of DXR from Thermooga maritia, in complex with fosmidomycin and NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZZ1 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · 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 Q9WZZ1
- Elsewhere: RCSB PDB 3A06 · PDBe 3A06 · UniProt Q9WZZ1
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