Research workbench
Crystal structure of dxr from thermooga maritia, in complex with fosmidomycin and NADPH
Analyse Crystal structure of dxr from thermooga maritia, in complex with fosmidomycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.