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Table 5 14 FEATURE predictions of which experimentally solved homologous holo structures are found through a homologous searching process using MAMMOTH

From: Prediction of calcium-binding sites by combining loop-modeling with machine learning

  Loop   FEATURE score   Holo structure Alignement
PDB ID Start End Sequence CaDis(Å) Gap Loop Ligand SCOP ID Start End Sequence CaDis(Å) PRA RMSD PID
1G57_B 33 39 DDED RE N 2.29 -29.15 62.92 CS d1pvwa_ 21 27 D SDE RE G 2.11 86 2.65 24
1VJS_A 181 193 AWD WE VSNE NGNY 2.49 41.99 82.70 None d1e40a2 178 193 E GKAWD WE VSSE NGNYD YLMY 2.18 97 1.06 66
2A9Q_A 53 59 LMLPE ID 3.34 44.10 57.51 None d1zh2b1 53 59 LGLPD GD 2.23 98 1.34 41
1GIH_A 149 164 ARAFGVPVRTYTHE VV 3.16 37.28 60.16 1PU d1u5ra_ 173 184 ASIMAPANFVG 2.47 81 3.03 19
1OZT_G 127 141 GKGGNEE STKTGNAG 1.71 23.67 61.66 None d1sxsb_ 125 139 GRGGNEE STKTGNAG 3.53 87 1.86 71
1LEW_A 173 183 RHTDDE MTGYV 2.20 10.16 71.76 None d2eufb1 170 180 YSFQMALTSVV 4.18 85 2.92 25
2JAV_A 131 141 SD GGHTVLHRD 2.60 8.93 56.86 5Z5 d2auha1 1123 1132 LNAKKFVHRD 4.87 85 3.06 16
2ANT_I 29 43 KATEDE GSE QKIPE A 2.23 20.71 80.94 NAA d1jmja_ 68 99 SEDD LQLFH 5.09 92 2.31 26
1U5I_A 563 568 KRED IK 2.97 39.39 66.52 None d1alwb_ 127 133 TRHPD LK 5.37 98 1.82 13
1EB7_A 222 229 ASVLPSGD 3.96 19.22 58.45 CA,HEC d1iqca2 207 213 E TKNPAA 6.58 86 1.79 21
1ANT_L 395 406 LNPNRVTFKANR 2.95 42.78 77.77 None d1jmja_ 446 454 TQVRFTVD R 6.64 88 2.72 26
2IYN_C 84 97 ARGEEED RVRGLE T 3.26 35.10 52.26 MG d1srrc_ 81 96 MTAYGE LD MIQE SKE L 6.88 96 2.7 25
2IK4_A 103 113 PNVSHPE TKAV 3.95 41.81 64.20 MG,PO4, d1i40a_ 59 63 NHTLS 4.03 91 3.49 13
  1. Column 1 lists PDB code followed by the chain identifier. We build structures for gaps of which 3D structures are not present in the original PDB files. Information of these structures, referred as "loop", is given in column 2-5. Column 5 lists the distances from the predicted sites to the rebuilt loops (CaDis). Column 6 and 7 list FEATURE scores at the predicted sites in the structures where loop structures are missing (Gap) and in the rebuilt loop structures (Loop). Ligands observed experimentally are listed in column 8 and the ligand IDs are from PDB. Column 9 shows the SCOP ID of the homologous holo structures. Information of aligned counterparts for the binding loops is listed in column 10-13. Column 13 lists the distances from the calcium ions to the aligned loop counterparts (CaDis). The percentage of residues aligned (PRA), the RMSD of the aligned regions, and the percentage of identical residues (PID) are shown in column 14-16.