In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or t...In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phos- phorus-related kinases (96%) from current PDB could go through the penta-coordinated phos- phorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 ?from the phosphorus atom, and a potential TBP structure consisting GNP2 and NZ could be overlapped with an authentic TBP with an RMSD value of 0.71 ?.展开更多
基金This work was supported by the National Natural Science Foundation of China(Grant No.20132020)the Ministry of Science and Technology,the Ministry of Education and Tsinghua University.
文摘In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phos- phorus-related kinases (96%) from current PDB could go through the penta-coordinated phos- phorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 ?from the phosphorus atom, and a potential TBP structure consisting GNP2 and NZ could be overlapped with an authentic TBP with an RMSD value of 0.71 ?.
