5cst

Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine diphosphate at 1.78 A resolution

spinqualitylabelsall models 5cst, resolution 1.78Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5cst is a 1 chain structure with sequence from Momordica balsamina. This structure supersedes the now removed PDB entries 4k6p, 4qgj and 4zw4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.78Å Ligands: CDP, GOL, NAG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D9J2T9_MOMBA Publication Abstract from PubMed The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10(-4) M-10(-7) M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors. Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with cytosine, cytidine, and cytidine diphosphate.,Yamini S, Pandey SN, Kaur P, Sharma S, Singh TP Biochem Biophys Rep. 2015 Sep 11;4:134-140. doi: 10.1016/j.bbrep.2015.09.006., eCollection 2015 Dec. PMID:29124196 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosome inactivating protein 3D structures

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