MolNFT v1 · #19974 · protein
Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis
1R0K: “Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from zymomonas mobilis”. X-ray diffraction, 18 pockets (best druggability 0.67). MolNFT v1 #19974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1R0K
- Type
- protein
- Length
- 1,521 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
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 50% 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 | 380 | 50% helix, 17% strand | Q9X5F2 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 382 | 49% helix, 16% strand | Q9X5F2 |
| C | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 379 | 49% helix, 17% strand | Q9X5F2 |
| D | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 380 | 50% helix, 17% strand | Q9X5F2 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.67 | 0.77 | 68 | empty |
| 2 | 461 | 0.66 | 0.78 | 33 | empty |
| 3 | 578 | 0.66 | 0.76 | 58 | empty |
| 4 | 472 | 0.66 | 0.78 | 34 | empty |
| 5 | 384 | 0.62 | 0.78 | 59 | ACT |
Interfaces
3 interfaces between chains.
- C–D · 1816 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1764 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1R0K · Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas… · 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 0.99
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 1R0K · PDBe 1R0K · UniProt Q9X5F2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.