6W70

Crystal Structure of apixaban-bound ABLE

Summary for 6W70

Entry DOI	10.2210/pdb6w70/pdb
Related	6W6X
Descriptor	De novo designed ABLE, SULFATE ION, ACETATE ION, ... (5 entities in total)
Functional Keywords	4-helix bundle, de novo, ligand-binding, de novo protein
Biological source	synthetic construct
Total number of polymer chains	2
Total formula weight	28768.12
Authors	Polizzi, N.F. (deposition date: 2020-03-18, release date: 2020-08-26, Last modification date: 2024-04-03)
Primary citation	Polizzi, N.F.,DeGrado, W.F. A defined structural unit enables de novo design of small-molecule-binding proteins. Science, 369:1227-1233, 2020 Cited by PubMed Abstract: The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis. PubMed: 32883865 DOI: 10.1126/science.abb8330 PDB entries with the same primary citation
Experimental method	X-RAY DIFFRACTION (1.296 Å)

Structure validation