Research workbench
Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) complexed with quinolin-2-ylmethylphosphonic acid
Analyse Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ANN
- 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, SYE
- Pockets
- 5 · best druggability 0.74
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 | 51% helix, 15% strand | P45568 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 398 | 51% helix, 15% strand | P45568 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SYE · (quinolin-2-ylmethyl)phosphonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.74 | 0.91 | 32 | empty |
| 2 | 651 | 0.74 | 0.80 | 73 | NDP, SYE |
| 3 | 589 | 0.74 | 0.81 | 66 | NDP, SYE |
| 4 | 87 | 0.36 | 0.75 | 19 | empty |
| 5 | 53 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1635 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3ANN · Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with… · the same entry in another collection · chain B against B, 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 3ANN · PDBe 3ANN · UniProt P45568
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