Plumbagin in complex with CRM1#-ran-RANBP1

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 8% strand (DSSP).

Ligands and binding sites

• F2X · (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione · ligand · 3 copies · chains C
• GTP · Guanosine-5'-triphosphate · ligand · chains A
• MG · Magnesium ion · metal · chains A
• NO3 · Nitrate ion · ion · 9 copies · chains A, C, B
• CL · Chloride ion · ion · 3 copies · chains C
• GOL · Glycerol · additive · 3 copies · chains A, C
• DMS · Dimethyl sulfoxide · additive · 3 copies · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 2048 Ų buried · 33 hydrogen bonds · protein-protein
• A–C · 1996 Ų buried · 27 hydrogen bonds · protein-protein
• B–C · 188 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

• 6M60 · Plumbagin in complex with CRM1#-Ran-RanBP1 · the same entry in another collection · chain A against A, TM-score 1.00
• P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B 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 P62826
• Every structure of UniProt P41920
• Every structure of UniProt P30822
• Elsewhere: RCSB PDB 6M60 · PDBe 6M60 · UniProt P62826 · UniProt P41920 · UniProt P30822