Research workbench
1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis in complex with NADPH
Analyse 1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R0L
- Type
- protein
- Length
- 1,513 residues
- Chains
- 4
- 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
- Q9X5F2
- Ligands
- NDP
- Pockets
- 17 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 378 | 49% helix, 17% strand | Q9X5F2 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 379 | 49% helix, 17% strand | Q9X5F2 |
| C | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 378 | 48% helix, 17% strand | Q9X5F2 |
| D | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 378 | 49% helix, 17% strand | Q9X5F2 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.66 | 0.78 | 33 | empty |
| 2 | 463 | 0.65 | 0.77 | 33 | empty |
| 3 | 426 | 0.61 | 0.76 | 59 | NDP |
| 4 | 375 | 0.60 | 0.77 | 57 | empty |
| 5 | 324 | 0.57 | 0.76 | 55 | NDP |
Interfaces
3 interfaces between chains.
- A–B · 1817 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1791 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1R0L · 1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9X5F2 · 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 0.98
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 Q9X5F2
- Elsewhere: RCSB PDB 1R0L · PDBe 1R0L · UniProt Q9X5F2
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