Research workbench
1-deoxy-D-xylulose 5-phosphate reductoisomerase from vibrio vulnificus in complex arginine
Analyse 1-deoxy-D-xylulose 5-phosphate reductoisomerase from vibrio vulnificus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KRV
- Type
- protein
- Length
- 787 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
- Q8DBF5
- Ligands
- ARG, SRT, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 394 | 51% helix, 15% strand | Q8DBF5 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 393 | 51% helix, 16% strand | Q8DBF5 |
Ligands and binding sites
- ARG · Arginine · ligand · chains A
- SRT · S,R meso-tartaric acid · ligand · chains B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 11 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.71 | 0.85 | 35 | EDO |
| 2 | 611 | 0.69 | 0.78 | 76 | EDO |
| 3 | 590 | 0.66 | 0.76 | 75 | EDO, CL |
| 4 | 53 | 0.44 | 0.84 | 15 | empty |
| 5 | 86 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1621 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5KRV · 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DBF5 · 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 0.95
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 Q8DBF5
- Elsewhere: RCSB PDB 5KRV · PDBe 5KRV · UniProt Q8DBF5
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