####################################################### # # # LGA # # --------------- # # # # Local-Global Alignment # # A Method for Finding 3-D Similarities # # in Protein Structures # # # # ------------ 09/2011 # # # # Adam Zemla (adamz@llnl.gov) # # Lawrence Livermore National Laboratory, CA # # # ####################################################### # Molecule1: number of CA atoms 21 ( 157), selected 21 , name T0970TS347_1 # Molecule2: number of CA atoms 85 ( 650), selected 21 , name T0970.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_1.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 21 55 - 75 2.25 2.25 LCS_AVERAGE: 24.71 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 19 56 - 74 1.96 2.32 LCS_AVERAGE: 22.24 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 15 55 - 69 0.76 4.71 LCS_AVERAGE: 14.68 LCS_GDT MOLECULE-1 MOLECULE-2 LCS_DETAILS GDT_DETAILS TOTAL NUMBER OF RESIDUE PAIRS: 21 LCS_GDT RESIDUE RESIDUE SEGMENT_SIZE GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair LCS_GDT NAME NUMBER NAME NUMBER 1.0 2.0 5.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 LCS_GDT E 55 E 55 15 18 21 8 13 15 15 16 16 17 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT Q 56 Q 56 15 19 21 8 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 57 A 57 15 19 21 8 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 58 F 58 15 19 21 8 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT D 59 D 59 15 19 21 8 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT R 60 R 60 15 19 21 8 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT L 61 L 61 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 62 S 62 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT E 63 E 63 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 64 A 64 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 65 G 65 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 66 F 66 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT H 67 H 67 15 19 21 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT M 68 M 68 15 19 21 9 12 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT V 69 V 69 15 19 21 9 11 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 70 A 70 12 19 21 3 9 12 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT C 71 C 71 6 19 21 3 7 12 14 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT N 72 N 72 6 19 21 3 5 8 12 15 15 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 73 S 73 6 19 21 3 7 11 14 15 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 74 S 74 4 19 21 3 7 12 14 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 75 G 75 3 18 21 3 3 3 6 7 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 LCS_AVERAGE LCS_A: 20.54 ( 14.68 22.24 24.71 ) GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds) GDT DIST_CUTOFF 0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 4.50 5.00 5.50 6.00 6.50 7.00 7.50 8.00 8.50 9.00 9.50 10.00 GDT NUMBER_AT 9 13 15 15 16 19 20 21 21 21 21 21 21 21 21 21 21 21 21 21 GDT PERCENT_AT 10.59 15.29 17.65 17.65 18.82 22.35 23.53 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 24.71 GDT RMS_LOCAL 0.31 0.52 0.76 0.76 1.15 1.98 2.08 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 GDT RMS_ALL_AT 4.38 5.35 4.71 4.71 3.88 2.27 2.27 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 # Checking swapping # possible swapping detected: E 55 E 55 # possible swapping detected: F 58 F 58 # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all Dist_at LGA E 55 E 55 4.138 0 0.290 1.274 5.405 10.909 5.455 4.610 LGA Q 56 Q 56 2.401 0 0.026 0.192 3.055 43.182 35.758 2.065 LGA A 57 A 57 1.636 0 0.053 0.055 2.296 54.545 51.273 - LGA F 58 F 58 2.408 0 0.024 0.072 5.480 44.545 20.165 5.409 LGA D 59 D 59 2.343 0 0.063 0.124 3.878 41.364 28.182 3.761 LGA R 60 R 60 1.291 0 0.024 1.274 6.514 61.818 39.008 5.251 LGA L 61 L 61 0.742 0 0.006 0.141 2.478 90.909 69.545 2.478 LGA S 62 S 62 0.835 0 0.000 0.630 3.571 78.182 64.848 3.571 LGA E 63 E 63 1.904 0 0.061 0.149 2.596 45.455 42.828 2.335 LGA A 64 A 64 2.065 0 0.105 0.114 2.899 38.636 41.091 - LGA G 65 G 65 1.752 0 0.049 0.049 1.752 58.182 58.182 - LGA F 66 F 66 0.462 0 0.041 0.110 2.752 90.909 64.132 2.752 LGA H 67 H 67 0.831 0 0.158 0.150 1.215 73.636 80.364 0.627 LGA M 68 M 68 2.371 0 0.085 1.360 7.022 41.364 24.773 7.022 LGA V 69 V 69 2.048 0 0.056 0.067 2.760 44.545 42.078 1.979 LGA A 70 A 70 1.180 0 0.108 0.142 1.704 61.818 65.818 - LGA C 71 C 71 2.127 0 0.080 0.764 5.393 33.636 25.455 5.393 LGA N 72 N 72 3.562 0 0.245 1.221 5.156 18.636 12.727 5.156 LGA S 73 S 73 3.013 0 0.039 0.578 3.268 22.727 24.545 2.235 LGA S 74 S 74 2.594 0 0.072 0.585 4.481 30.909 23.333 3.789 LGA G 75 G 75 3.172 0 0.146 0.146 5.410 17.273 17.273 - # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all GDC_at NUMBER_OF_ATOMS_AA: 21 84 84 100.00 156 156 100.00 85 16 SUMMARY(RMSD_GDC): 2.246 2.265 2.849 11.802 9.845 21.705 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 21 85 4.0 21 2.25 20.588 21.726 0.895 LGA_LOCAL RMSD: 2.246 Number of atoms: 21 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 2.246 Number of assigned atoms: 21 Std_ASGN_ATOMS RMSD: 2.246 Standard rmsd on all 21 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.769707 * X + 0.564606 * Y + -0.297944 * Z + 45.957596 Y_new = -0.591177 * X + 0.454233 * Y + -0.666470 * Z + -12.970029 Z_new = -0.240957 * X + 0.689124 * Y + 0.683409 * Z + 48.194645 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -0.654956 0.243352 0.789562 [DEG: -37.5262 13.9430 45.2386 ] ZXZ: -0.420396 0.818375 -0.336369 [DEG: -24.0869 46.8894 -19.2725 ] # END of job REMARK ---------------------------------------------------------- REMARK Citing LGA: REMARK Zemla A., LGA - a Method for Finding 3D Similarities in REMARK Protein Structures, Nucleic Acids Research, 2003, V. 31, REMARK No. 13, pp. 3370-3374. REMARK ---------------------------------------------------------- REMARK Superimposed MOLECULES (1=>2) Output: 1 molecule REMARK 1: T0970TS347_1 REMARK 2: T0970.pdb REMARK GDT and LCS analysis REMARK FIXED Atom-Atom correspondence REMARK LGA parameters: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_1.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 21 85 4.0 21 2.25 21.726 2.25 REMARK ---------------------------------------------------------- MOLECULE T0970TS347_1 PFRMAT TS TARGET T0970 MODEL 1 PARENT 1wpl_R 1jg5_B ATOM 1 N GLU 55 62.632 37.216 92.731 1.00 4.54 ATOM 0 CA GLU 55 63.484 37.549 93.889 1.00 4.54 ATOM 2 CB GLU 55 62.688 37.448 95.193 1.00 4.54 ATOM 3 C GLU 55 64.694 36.624 93.948 1.00 4.54 ATOM 4 O GLU 55 65.727 36.899 93.333 1.00 4.54 ATOM 5 CG GLU 55 63.427 37.987 96.409 1.00 4.54 ATOM 6 CD GLU 55 63.565 39.500 96.403 1.00 4.54 ATOM 7 OE1 GLU 55 62.594 40.188 96.015 1.00 4.54 ATOM 8 OE2 GLU 55 64.645 40.004 96.783 1.00 4.54 ATOM 10 N GLN 56 64.578 35.533 94.699 1.00 3.49 ATOM 9 CA GLN 56 65.670 34.571 94.810 1.00 3.49 ATOM 12 CB GLN 56 65.294 33.446 95.778 1.00 3.49 ATOM 13 C GLN 56 66.010 33.984 93.445 1.00 3.49 ATOM 14 O GLN 56 67.185 33.823 93.106 1.00 3.49 ATOM 15 CG GLN 56 65.134 33.904 97.221 1.00 3.49 ATOM 16 CD GLN 56 64.825 32.758 98.166 1.00 3.49 ATOM 17 NE2 GLN 56 65.367 32.821 99.377 1.00 3.49 ATOM 20 OE1 GLN 56 64.110 31.817 97.807 1.00 3.49 ATOM 22 N ALA 57 64.984 33.687 92.653 1.00 2.67 ATOM 21 CA ALA 57 65.192 33.155 91.310 1.00 2.67 ATOM 24 CB ALA 57 63.852 32.817 90.661 1.00 2.67 ATOM 25 C ALA 57 65.947 34.161 90.448 1.00 2.67 ATOM 26 O ALA 57 66.892 33.799 89.745 1.00 2.67 ATOM 28 N PHE 58 65.542 35.426 90.514 1.00 2.06 ATOM 27 CA PHE 58 66.200 36.474 89.741 1.00 2.06 ATOM 30 CB PHE 58 65.430 37.797 89.844 1.00 2.06 ATOM 31 C PHE 58 67.640 36.662 90.205 1.00 2.06 ATOM 32 O PHE 58 68.533 36.906 89.391 1.00 2.06 ATOM 33 CG PHE 58 64.107 37.773 89.122 1.00 2.06 ATOM 34 CD1 PHE 58 63.126 38.706 89.438 1.00 2.06 ATOM 35 CE1 PHE 58 61.908 38.689 88.764 1.00 2.06 ATOM 36 CZ PHE 58 61.677 37.745 87.772 1.00 2.06 ATOM 37 CD2 PHE 58 63.862 36.807 88.153 1.00 2.06 ATOM 38 CE2 PHE 58 62.641 36.789 87.483 1.00 2.06 ATOM 40 N ASP 59 67.870 36.525 91.506 1.00 1.96 ATOM 39 CA ASP 59 69.219 36.643 92.051 1.00 1.96 ATOM 42 CB ASP 59 69.182 36.617 93.582 1.00 1.96 ATOM 43 C ASP 59 70.105 35.519 91.526 1.00 1.96 ATOM 44 O ASP 59 71.234 35.761 91.092 1.00 1.96 ATOM 45 CG ASP 59 68.630 37.897 94.180 1.00 1.96 ATOM 46 OD1 ASP 59 68.498 38.896 93.440 1.00 1.96 ATOM 47 OD2 ASP 59 68.332 37.915 95.394 1.00 1.96 ATOM 49 N ARG 60 69.593 34.292 91.543 1.00 1.53 ATOM 48 CA ARG 60 70.341 33.149 91.029 1.00 1.53 ATOM 51 CB ARG 60 69.595 31.841 91.308 1.00 1.53 ATOM 52 C ARG 60 70.572 33.304 89.530 1.00 1.53 ATOM 53 O ARG 60 71.667 33.035 89.032 1.00 1.53 ATOM 54 CG ARG 60 68.958 31.223 90.073 1.00 1.53 ATOM 55 CD ARG 60 68.420 29.827 90.356 1.00 1.53 ATOM 56 NE ARG 60 67.137 29.599 89.696 1.00 1.53 ATOM 58 CZ ARG 60 66.987 29.309 88.407 1.00 1.53 ATOM 59 NH1 ARG 60 65.772 29.119 87.902 1.00 1.53 ATOM 60 NH2 ARG 60 68.051 29.198 87.618 1.00 1.53 ATOM 62 N LEU 61 69.546 33.754 88.815 1.00 1.13 ATOM 61 CA LEU 61 69.662 33.983 87.379 1.00 1.13 ATOM 64 CB LEU 61 68.315 34.426 86.797 1.00 1.13 ATOM 65 C LEU 61 70.720 35.047 87.111 1.00 1.13 ATOM 66 O LEU 61 71.457 34.967 86.125 1.00 1.13 ATOM 67 CG LEU 61 67.234 33.347 86.687 1.00 1.13 ATOM 68 CD1 LEU 61 65.954 33.943 86.119 1.00 1.13 ATOM 69 CD2 LEU 61 67.724 32.200 85.815 1.00 1.13 ATOM 71 N SER 62 70.807 36.033 87.997 1.00 1.52 ATOM 70 CA SER 62 71.812 37.082 87.870 1.00 1.52 ATOM 73 CB SER 62 71.661 38.106 88.998 1.00 1.52 ATOM 74 C SER 62 73.214 36.487 87.910 1.00 1.52 ATOM 75 O SER 62 74.075 36.851 87.107 1.00 1.52 ATOM 76 OG SER 62 70.379 38.712 88.957 1.00 1.52 ATOM 78 N GLU 63 73.439 35.562 88.839 1.00 2.89 ATOM 77 CA GLU 63 74.734 34.898 88.935 1.00 2.89 ATOM 80 CB GLU 63 74.760 33.951 90.139 1.00 2.89 ATOM 81 C GLU 63 75.024 34.119 87.658 1.00 2.89 ATOM 82 O GLU 63 76.177 34.013 87.234 1.00 2.89 ATOM 83 CG GLU 63 74.756 34.665 91.484 1.00 2.89 ATOM 84 CD GLU 63 74.868 33.716 92.665 1.00 2.89 ATOM 85 OE1 GLU 63 74.883 32.485 92.445 1.00 2.89 ATOM 86 OE2 GLU 63 74.947 34.201 93.816 1.00 2.89 ATOM 88 N ALA 64 73.975 33.585 87.039 1.00 3.32 ATOM 87 CA ALA 64 74.121 32.845 85.790 1.00 3.32 ATOM 90 CB ALA 64 72.867 32.020 85.517 1.00 3.32 ATOM 91 C ALA 64 74.391 33.792 84.623 1.00 3.32 ATOM 92 O ALA 64 75.006 33.401 83.628 1.00 3.32 ATOM 94 N GLY 65 73.937 35.035 84.748 1.00 3.07 ATOM 93 CA GLY 65 74.144 36.023 83.702 1.00 3.07 ATOM 96 C GLY 65 72.853 36.465 83.037 1.00 3.07 ATOM 97 O GLY 65 72.877 37.264 82.097 1.00 3.07 ATOM 99 N PHE 66 71.721 35.966 83.524 1.00 1.81 ATOM 98 CA PHE 66 70.422 36.340 82.975 1.00 1.81 ATOM 101 CB PHE 66 69.336 35.368 83.453 1.00 1.81 ATOM 102 C PHE 66 70.055 37.763 83.380 1.00 1.81 ATOM 103 O PHE 66 70.342 38.189 84.500 1.00 1.81 ATOM 104 CG PHE 66 69.496 33.970 82.915 1.00 1.81 ATOM 105 CD1 PHE 66 70.333 33.067 83.560 1.00 1.81 ATOM 106 CE1 PHE 66 70.492 31.780 83.052 1.00 1.81 ATOM 107 CZ PHE 66 69.805 31.395 81.908 1.00 1.81 ATOM 108 CD2 PHE 66 68.797 33.579 81.778 1.00 1.81 ATOM 109 CE2 PHE 66 68.950 32.288 81.277 1.00 1.81 ATOM 111 N HIS 67 69.436 38.500 82.464 1.00 1.32 ATOM 110 CA HIS 67 69.017 39.869 82.740 1.00 1.32 ATOM 113 CB HIS 67 69.806 40.851 81.867 1.00 1.32 ATOM 114 C HIS 67 67.522 40.041 82.499 1.00 1.32 ATOM 115 O HIS 67 67.066 40.029 81.354 1.00 1.32 ATOM 116 CG HIS 67 71.289 40.651 81.963 1.00 1.32 ATOM 117 ND1 HIS 67 72.012 41.022 83.073 1.00 1.32 ATOM 119 CE1 HIS 67 73.271 40.693 82.831 1.00 1.32 ATOM 120 NE2 HIS 67 73.382 40.105 81.652 1.00 1.32 ATOM 122 CD2 HIS 67 72.132 40.053 81.086 1.00 1.32 ATOM 124 N MET 68 66.756 40.211 83.572 1.00 2.48 ATOM 123 CA MET 68 65.308 40.351 83.458 1.00 2.48 ATOM 126 CB MET 68 64.678 40.578 84.836 1.00 2.48 ATOM 127 C MET 68 64.941 41.497 82.522 1.00 2.48 ATOM 128 O MET 68 65.093 42.669 82.874 1.00 2.48 ATOM 129 CG MET 68 65.044 39.510 85.855 1.00 2.48 ATOM 130 SD MET 68 65.145 37.864 85.116 1.00 2.48 ATOM 131 CE MET 68 63.500 37.704 84.440 1.00 2.48 ATOM 133 N VAL 69 64.437 41.160 81.340 1.00 3.74 ATOM 132 CA VAL 69 64.079 42.168 80.348 1.00 3.74 ATOM 135 CB VAL 69 63.356 41.532 79.139 1.00 3.74 ATOM 136 C VAL 69 63.194 43.236 80.984 1.00 3.74 ATOM 137 O VAL 69 63.373 44.429 80.727 1.00 3.74 ATOM 138 CG1 VAL 69 62.911 42.609 78.156 1.00 3.74 ATOM 139 CG2 VAL 69 64.267 40.524 78.445 1.00 3.74 ATOM 141 N ALA 70 62.235 42.817 81.804 1.00 3.73 ATOM 140 CA ALA 70 61.323 43.762 82.444 1.00 3.73 ATOM 143 CB ALA 70 60.194 44.133 81.487 1.00 3.73 ATOM 144 C ALA 70 60.747 43.198 83.738 1.00 3.73 ATOM 145 O ALA 70 60.238 42.074 83.762 1.00 3.73 ATOM 147 N CYS 71 60.818 43.980 84.811 1.00 2.36 ATOM 146 CA CYS 71 60.274 43.565 86.099 1.00 2.36 ATOM 149 CB CYS 71 61.331 42.802 86.903 1.00 2.36 ATOM 150 C CYS 71 59.798 44.775 86.894 1.00 2.36 ATOM 151 O CYS 71 60.478 45.802 86.933 1.00 2.36 ATOM 152 SG CYS 71 61.573 41.093 86.355 1.00 2.36 ATOM 154 N ASN 72 58.628 44.661 87.520 1.00 2.43 ATOM 153 CA ASN 72 58.063 45.768 88.286 1.00 2.43 ATOM 156 CB ASN 72 57.122 46.598 87.406 1.00 2.43 ATOM 157 C ASN 72 57.321 45.271 89.520 1.00 2.43 ATOM 158 O ASN 72 57.052 44.074 89.651 1.00 2.43 ATOM 159 CG ASN 72 55.872 45.837 87.008 1.00 2.43 ATOM 160 ND2 ASN 72 55.636 45.719 85.708 1.00 2.43 ATOM 163 OD1 ASN 72 55.127 45.353 87.864 1.00 2.43 ATOM 165 N SER 73 57.001 46.184 90.431 1.00 3.44 ATOM 164 CA SER 73 56.269 45.828 91.642 1.00 3.44 ATOM 167 CB SER 73 56.941 46.447 92.870 1.00 3.44 ATOM 168 C SER 73 54.818 46.287 91.564 1.00 3.44 ATOM 169 O SER 73 54.498 47.228 90.832 1.00 3.44 ATOM 170 OG SER 73 56.814 47.859 92.852 1.00 3.44 ATOM 172 N SER 74 53.941 45.639 92.325 1.00 4.88 ATOM 171 CA SER 74 52.524 45.984 92.311 1.00 4.88 ATOM 174 CB SER 74 51.751 45.097 93.292 1.00 4.88 ATOM 175 C SER 74 52.308 47.451 92.665 1.00 4.88 ATOM 176 O SER 74 52.792 47.925 93.696 1.00 4.88 ATOM 177 OG SER 74 50.372 45.427 93.285 1.00 4.88 ATOM 179 N GLY 75 51.573 48.165 91.820 1.00 6.26 ATOM 178 CA GLY 75 51.318 49.577 92.054 1.00 6.26 ATOM 181 C GLY 75 51.678 50.439 90.853 1.00 6.26 ATOM 182 O GLY 75 51.898 49.880 89.759 1.00 6.26 ATOM 183 OXT GLY 75 51.741 51.677 91.001 1.00 6.26 TER END