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1SNC

THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS

Summary for 1SNC
Entry DOI10.2210/pdb1snc/pdb
DescriptorTHERMONUCLEASE PRECURSOR, CALCIUM ION, THYMIDINE-3',5'-DIPHOSPHATE, ... (4 entities in total)
Functional Keywordshydrolase (phosphoric diester)
Biological sourceStaphylococcus aureus
Cellular locationNuclease A: Secreted. Nuclease B: Membrane: P00644
Total number of polymer chains1
Total formula weight17285.60
Authors
Loll, P.J.,Lattman, E.E. (deposition date: 1989-07-21, release date: 1990-10-15, Last modification date: 2024-02-14)
Primary citationLoll, P.J.,Lattman, E.E.
The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A.
Proteins, 5:183-201, 1989
Cited by
PubMed Abstract: The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.
PubMed: 2780539
DOI: 10.1002/prot.340050302
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.65 Å)
Structure validation

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