####################################################### # # # 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_5 # Molecule2: number of CA atoms 85 ( 650), selected 21 , name T0970.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_5.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 2.34 2.34 LCS_AVERAGE: 24.71 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 19 55 - 73 1.92 2.62 LONGEST_CONTINUOUS_SEGMENT: 19 56 - 74 1.91 2.46 LCS_AVERAGE: 22.18 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 15 55 - 69 0.80 5.27 LCS_AVERAGE: 14.85 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 19 21 10 13 14 15 16 17 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT Q 56 Q 56 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 57 A 57 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 58 F 58 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT D 59 D 59 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT R 60 R 60 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT L 61 L 61 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 62 S 62 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT E 63 E 63 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 64 A 64 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 65 G 65 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT F 66 F 66 15 19 21 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT H 67 H 67 15 19 21 9 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT M 68 M 68 15 19 21 9 11 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT V 69 V 69 15 19 21 9 11 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT A 70 A 70 7 19 21 3 8 11 14 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT C 71 C 71 7 19 21 3 8 11 14 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT N 72 N 72 7 19 21 3 7 11 14 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 73 S 73 7 19 21 3 5 10 14 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT S 74 S 74 7 19 21 3 5 10 13 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 LCS_GDT G 75 G 75 5 16 21 3 3 5 7 8 11 14 15 20 21 21 21 21 21 21 21 21 21 21 21 LCS_AVERAGE LCS_A: 20.58 ( 14.85 22.18 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 10 13 14 15 16 19 19 20 20 21 21 21 21 21 21 21 21 21 21 21 GDT PERCENT_AT 11.76 15.29 16.47 17.65 18.82 22.35 22.35 23.53 23.53 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 0.37 0.52 0.67 0.80 1.28 1.91 1.91 2.06 2.06 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 GDT RMS_ALL_AT 6.06 5.59 5.57 5.27 4.23 2.46 2.46 2.43 2.43 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 # 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 3.643 0 0.212 0.923 4.564 17.727 18.384 2.539 LGA Q 56 Q 56 1.673 0 0.028 0.121 2.386 59.091 59.394 1.283 LGA A 57 A 57 1.628 0 0.039 0.044 2.295 54.545 51.273 - LGA F 58 F 58 1.958 0 0.015 0.170 4.539 58.182 29.256 4.539 LGA D 59 D 59 1.708 0 0.059 0.161 3.220 54.545 41.136 2.758 LGA R 60 R 60 1.213 0 0.050 1.373 6.546 65.909 37.521 5.368 LGA L 61 L 61 1.145 0 0.000 0.045 2.678 73.636 56.591 2.555 LGA S 62 S 62 0.696 0 0.026 0.189 1.478 78.182 76.667 1.116 LGA E 63 E 63 1.779 0 0.082 0.178 2.721 45.455 48.485 1.716 LGA A 64 A 64 2.312 0 0.099 0.108 3.204 36.364 36.727 - LGA G 65 G 65 1.981 0 0.100 0.100 1.981 54.545 54.545 - LGA F 66 F 66 0.820 0 0.039 0.179 3.619 81.818 49.587 3.619 LGA H 67 H 67 1.066 0 0.084 0.090 1.560 65.909 67.455 1.402 LGA M 68 M 68 2.955 0 0.000 1.243 6.804 30.000 17.045 6.804 LGA V 69 V 69 2.852 0 0.022 0.028 4.191 32.727 24.675 3.209 LGA A 70 A 70 1.618 0 0.014 0.017 1.754 50.909 53.818 - LGA C 71 C 71 1.905 0 0.183 0.858 3.642 50.909 42.121 3.642 LGA N 72 N 72 1.942 0 0.185 0.301 5.103 39.545 24.773 3.863 LGA S 73 S 73 2.221 0 0.035 0.579 5.006 59.091 42.424 5.006 LGA S 74 S 74 3.141 0 0.093 0.130 7.726 9.545 6.364 7.726 LGA G 75 G 75 6.274 0 0.079 0.079 6.274 4.091 4.091 - # 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): 2.336 2.282 2.823 12.032 9.910 23.864 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 21 85 4.0 20 2.06 20.294 21.439 0.927 LGA_LOCAL RMSD: 2.058 Number of atoms: 20 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 2.430 Number of assigned atoms: 21 Std_ASGN_ATOMS RMSD: 2.336 Standard rmsd on all 21 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.780161 * X + 0.495136 * Y + 0.382347 * Z + 8.608831 Y_new = -0.622911 * X + 0.558465 * Y + 0.547812 * Z + 3.397147 Z_new = 0.057714 * X + -0.665550 * Y + 0.744119 * Z + 117.928528 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -0.673789 -0.057746 -0.729720 [DEG: -38.6052 -3.3086 -41.8099 ] ZXZ: 2.532242 0.731582 3.055093 [DEG: 145.0868 41.9166 175.0439 ] # 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_5 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_5.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 21 85 4.0 20 2.06 21.439 2.34 REMARK ---------------------------------------------------------- MOLECULE T0970TS347_5 PFRMAT TS TARGET T0970 MODEL 5 PARENT 1wpl_R 1jg5_B ATOM 1 N GLU 55 62.828 36.298 93.430 1.00 3.83 ATOM 0 CA GLU 55 63.843 36.919 94.303 1.00 3.83 ATOM 2 CB GLU 55 63.345 36.983 95.750 1.00 3.83 ATOM 3 C GLU 55 65.152 36.141 94.240 1.00 3.83 ATOM 4 O GLU 55 66.107 36.570 93.588 1.00 3.83 ATOM 5 CG GLU 55 64.266 37.752 96.684 1.00 3.83 ATOM 6 CD GLU 55 63.780 37.770 98.123 1.00 3.83 ATOM 7 OE1 GLU 55 62.593 37.450 98.358 1.00 3.83 ATOM 8 OE2 GLU 55 64.582 38.107 99.022 1.00 3.83 ATOM 10 N GLN 56 65.210 35.005 94.929 1.00 2.58 ATOM 9 CA GLN 56 66.406 34.171 94.904 1.00 2.58 ATOM 12 CB GLN 56 66.265 33.012 95.895 1.00 2.58 ATOM 13 C GLN 56 66.642 33.624 93.502 1.00 2.58 ATOM 14 O GLN 56 67.787 33.463 93.074 1.00 2.58 ATOM 15 CG GLN 56 66.239 33.450 97.352 1.00 2.58 ATOM 16 CD GLN 56 65.928 32.307 98.299 1.00 2.58 ATOM 17 NE2 GLN 56 66.575 32.300 99.460 1.00 2.58 ATOM 20 OE1 GLN 56 65.108 31.435 97.992 1.00 2.58 ATOM 22 N ALA 57 65.558 33.315 92.796 1.00 2.23 ATOM 21 CA ALA 57 65.671 32.833 91.423 1.00 2.23 ATOM 24 CB ALA 57 64.286 32.526 90.858 1.00 2.23 ATOM 25 C ALA 57 66.352 33.901 90.574 1.00 2.23 ATOM 26 O ALA 57 67.211 33.598 89.741 1.00 2.23 ATOM 28 N PHE 58 65.976 35.155 90.806 1.00 1.58 ATOM 27 CA PHE 58 66.577 36.274 90.091 1.00 1.58 ATOM 30 CB PHE 58 65.855 37.583 90.436 1.00 1.58 ATOM 31 C PHE 58 68.056 36.388 90.442 1.00 1.58 ATOM 32 O PHE 58 68.896 36.579 89.560 1.00 1.58 ATOM 33 CG PHE 58 64.450 37.660 89.900 1.00 1.58 ATOM 34 CD1 PHE 58 63.654 38.762 90.191 1.00 1.58 ATOM 35 CE1 PHE 58 62.352 38.830 89.701 1.00 1.58 ATOM 36 CZ PHE 58 61.854 37.802 88.911 1.00 1.58 ATOM 37 CD2 PHE 58 63.944 36.623 89.124 1.00 1.58 ATOM 38 CE2 PHE 58 62.641 36.692 88.636 1.00 1.58 ATOM 40 N ASP 59 68.379 36.253 91.723 1.00 1.39 ATOM 39 CA ASP 59 69.768 36.317 92.163 1.00 1.39 ATOM 42 CB ASP 59 69.848 36.216 93.690 1.00 1.39 ATOM 43 C ASP 59 70.584 35.198 91.524 1.00 1.39 ATOM 44 O ASP 59 71.692 35.428 91.037 1.00 1.39 ATOM 45 CG ASP 59 69.281 37.435 94.393 1.00 1.39 ATOM 46 OD1 ASP 59 68.938 38.420 93.703 1.00 1.39 ATOM 47 OD2 ASP 59 69.185 37.419 95.639 1.00 1.39 ATOM 49 N ARG 60 70.035 33.987 91.518 1.00 1.59 ATOM 48 CA ARG 60 70.707 32.847 90.905 1.00 1.59 ATOM 51 CB ARG 60 69.857 31.582 91.055 1.00 1.59 ATOM 52 C ARG 60 70.963 33.120 89.427 1.00 1.59 ATOM 53 O ARG 60 72.069 32.898 88.928 1.00 1.59 ATOM 54 CG ARG 60 70.109 30.542 89.974 1.00 1.59 ATOM 55 CD ARG 60 69.289 29.280 90.203 1.00 1.59 ATOM 56 NE ARG 60 68.012 29.327 89.499 1.00 1.59 ATOM 58 CZ ARG 60 67.860 29.159 88.187 1.00 1.59 ATOM 59 NH1 ARG 60 66.650 29.221 87.642 1.00 1.59 ATOM 60 NH2 ARG 60 68.916 28.916 87.418 1.00 1.59 ATOM 62 N LEU 61 69.946 33.617 88.732 1.00 1.37 ATOM 61 CA LEU 61 70.065 33.916 87.309 1.00 1.37 ATOM 64 CB LEU 61 68.703 34.323 86.736 1.00 1.37 ATOM 65 C LEU 61 71.088 35.022 87.073 1.00 1.37 ATOM 66 O LEU 61 71.782 35.024 86.055 1.00 1.37 ATOM 67 CG LEU 61 67.670 33.201 86.610 1.00 1.37 ATOM 68 CD1 LEU 61 66.290 33.782 86.338 1.00 1.37 ATOM 69 CD2 LEU 61 68.077 32.242 85.497 1.00 1.37 ATOM 71 N SER 62 71.179 35.965 88.005 1.00 1.62 ATOM 70 CA SER 62 72.157 37.040 87.895 1.00 1.62 ATOM 73 CB SER 62 72.028 38.006 89.077 1.00 1.62 ATOM 74 C SER 62 73.567 36.462 87.860 1.00 1.62 ATOM 75 O SER 62 74.416 36.920 87.092 1.00 1.62 ATOM 76 OG SER 62 72.806 37.558 90.174 1.00 1.62 ATOM 78 N GLU 63 73.807 35.439 88.675 1.00 3.00 ATOM 77 CA GLU 63 75.109 34.783 88.697 1.00 3.00 ATOM 80 CB GLU 63 75.163 33.747 89.825 1.00 3.00 ATOM 81 C GLU 63 75.397 34.110 87.360 1.00 3.00 ATOM 82 O GLU 63 76.532 34.129 86.881 1.00 3.00 ATOM 83 CG GLU 63 75.007 34.343 91.216 1.00 3.00 ATOM 84 CD GLU 63 75.105 33.310 92.324 1.00 3.00 ATOM 85 OE1 GLU 63 75.130 32.098 92.014 1.00 3.00 ATOM 86 OE2 GLU 63 75.167 33.708 93.509 1.00 3.00 ATOM 88 N ALA 64 74.370 33.523 86.752 1.00 3.46 ATOM 87 CA ALA 64 74.520 32.876 85.453 1.00 3.46 ATOM 90 CB ALA 64 73.270 32.060 85.132 1.00 3.46 ATOM 91 C ALA 64 74.757 33.913 84.360 1.00 3.46 ATOM 92 O ALA 64 75.348 33.607 83.321 1.00 3.46 ATOM 94 N GLY 65 74.288 35.135 84.590 1.00 3.15 ATOM 93 CA GLY 65 74.429 36.197 83.608 1.00 3.15 ATOM 96 C GLY 65 73.106 36.604 82.986 1.00 3.15 ATOM 97 O GLY 65 73.039 37.589 82.247 1.00 3.15 ATOM 99 N PHE 66 72.046 35.861 83.290 1.00 1.85 ATOM 98 CA PHE 66 70.720 36.170 82.767 1.00 1.85 ATOM 101 CB PHE 66 69.770 34.982 82.966 1.00 1.85 ATOM 102 C PHE 66 70.150 37.410 83.446 1.00 1.85 ATOM 103 O PHE 66 70.359 37.620 84.642 1.00 1.85 ATOM 104 CG PHE 66 70.131 33.771 82.147 1.00 1.85 ATOM 105 CD1 PHE 66 70.860 32.735 82.722 1.00 1.85 ATOM 106 CE1 PHE 66 71.198 31.618 81.962 1.00 1.85 ATOM 107 CZ PHE 66 70.802 31.535 80.634 1.00 1.85 ATOM 108 CD2 PHE 66 69.731 33.685 80.819 1.00 1.85 ATOM 109 CE2 PHE 66 70.064 32.563 80.062 1.00 1.85 ATOM 111 N HIS 67 69.444 38.237 82.680 1.00 1.19 ATOM 110 CA HIS 67 68.840 39.449 83.222 1.00 1.19 ATOM 113 CB HIS 67 69.515 40.691 82.627 1.00 1.19 ATOM 114 C HIS 67 67.344 39.490 82.935 1.00 1.19 ATOM 115 O HIS 67 66.923 39.377 81.783 1.00 1.19 ATOM 116 CG HIS 67 71.007 40.671 82.775 1.00 1.19 ATOM 117 ND1 HIS 67 71.630 40.872 83.986 1.00 1.19 ATOM 119 CE1 HIS 67 72.931 40.774 83.762 1.00 1.19 ATOM 120 NE2 HIS 67 73.167 40.506 82.489 1.00 1.19 ATOM 122 CD2 HIS 67 71.959 40.424 81.842 1.00 1.19 ATOM 124 N MET 68 66.534 39.640 83.980 1.00 2.52 ATOM 123 CA MET 68 65.085 39.686 83.819 1.00 2.52 ATOM 126 CB MET 68 64.404 39.902 85.173 1.00 2.52 ATOM 127 C MET 68 64.682 40.794 82.852 1.00 2.52 ATOM 128 O MET 68 65.059 41.954 83.037 1.00 2.52 ATOM 129 CG MET 68 65.276 39.532 86.364 1.00 2.52 ATOM 130 SD MET 68 65.913 37.843 86.257 1.00 2.52 ATOM 131 CE MET 68 64.416 36.946 85.877 1.00 2.52 ATOM 133 N VAL 69 63.926 40.440 81.819 1.00 3.83 ATOM 132 CA VAL 69 63.503 41.414 80.818 1.00 3.83 ATOM 135 CB VAL 69 62.353 40.860 79.947 1.00 3.83 ATOM 136 C VAL 69 63.058 42.700 81.508 1.00 3.83 ATOM 137 O VAL 69 63.591 43.777 81.232 1.00 3.83 ATOM 138 CG1 VAL 69 61.809 41.947 79.027 1.00 3.83 ATOM 139 CG2 VAL 69 62.832 39.666 79.129 1.00 3.83 ATOM 141 N ALA 70 62.088 42.590 82.412 1.00 3.50 ATOM 140 CA ALA 70 61.581 43.755 83.129 1.00 3.50 ATOM 143 CB ALA 70 60.769 44.640 82.188 1.00 3.50 ATOM 144 C ALA 70 60.727 43.336 84.320 1.00 3.50 ATOM 145 O ALA 70 60.200 42.221 84.354 1.00 3.50 ATOM 147 N CYS 71 60.594 44.223 85.303 1.00 2.18 ATOM 146 CA CYS 71 59.778 43.940 86.479 1.00 2.18 ATOM 149 CB CYS 71 60.585 44.176 87.758 1.00 2.18 ATOM 150 C CYS 71 58.526 44.806 86.495 1.00 2.18 ATOM 151 O CYS 71 58.446 45.803 85.773 1.00 2.18 ATOM 152 SG CYS 71 61.869 42.933 88.052 1.00 2.18 ATOM 154 N ASN 72 57.544 44.422 87.308 1.00 2.65 ATOM 153 CA ASN 72 56.295 45.170 87.406 1.00 2.65 ATOM 156 CB ASN 72 55.133 44.224 87.725 1.00 2.65 ATOM 157 C ASN 72 56.386 46.263 88.465 1.00 2.65 ATOM 158 O ASN 72 57.119 46.123 89.447 1.00 2.65 ATOM 159 CG ASN 72 54.919 43.181 86.646 1.00 2.65 ATOM 160 ND2 ASN 72 55.009 41.911 87.020 1.00 2.65 ATOM 163 OD1 ASN 72 54.686 43.514 85.481 1.00 2.65 ATOM 165 N SER 73 55.640 47.346 88.273 1.00 2.61 ATOM 164 CA SER 73 55.642 48.449 89.229 1.00 2.61 ATOM 167 CB SER 73 56.348 49.669 88.632 1.00 2.61 ATOM 168 C SER 73 54.223 48.827 89.638 1.00 2.61 ATOM 169 O SER 73 53.272 48.599 88.886 1.00 2.61 ATOM 170 OG SER 73 55.590 50.213 87.564 1.00 2.61 ATOM 172 N SER 74 54.078 49.417 90.820 1.00 5.18 ATOM 171 CA SER 74 52.763 49.805 91.320 1.00 5.18 ATOM 174 CB SER 74 52.800 49.969 92.841 1.00 5.18 ATOM 175 C SER 74 52.285 51.102 90.676 1.00 5.18 ATOM 176 O SER 74 53.073 51.820 90.056 1.00 5.18 ATOM 177 OG SER 74 53.578 51.098 93.202 1.00 5.18 ATOM 179 N GLY 75 50.999 51.400 90.823 1.00 6.31 ATOM 178 CA GLY 75 50.442 52.621 90.264 1.00 6.31 ATOM 181 C GLY 75 48.938 52.528 90.051 1.00 6.31 ATOM 182 O GLY 75 48.374 51.431 90.239 1.00 6.31 ATOM 183 OXT GLY 75 48.318 53.553 89.699 1.00 6.31 TER END