####################################################### # # # 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_3 # Molecule2: number of CA atoms 85 ( 650), selected 21 , name T0970.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_3.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 2.54 2.54 LCS_AVERAGE: 24.71 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 20 55 - 74 1.58 2.73 LCS_AVERAGE: 22.63 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 15 55 - 69 0.84 2.71 LCS_AVERAGE: 16.08 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 20 21 8 13 14 16 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT Q 56 Q 56 15 20 21 8 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT A 57 A 57 15 20 21 8 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT F 58 F 58 15 20 21 8 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT D 59 D 59 15 20 21 8 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT R 60 R 60 15 20 21 8 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT L 61 L 61 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT S 62 S 62 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT E 63 E 63 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT A 64 A 64 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT G 65 G 65 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT F 66 F 66 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT H 67 H 67 15 20 21 9 13 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT M 68 M 68 15 20 21 9 12 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT V 69 V 69 15 20 21 7 12 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT A 70 A 70 14 20 21 5 7 14 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT C 71 C 71 14 20 21 5 7 14 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT N 72 N 72 14 20 21 5 11 14 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT S 73 S 73 14 20 21 9 12 15 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT S 74 S 74 3 20 21 3 3 6 15 17 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 LCS_GDT G 75 G 75 3 4 21 3 3 3 3 4 5 7 7 8 10 12 17 18 19 21 21 21 21 21 21 LCS_AVERAGE LCS_A: 21.14 ( 16.08 22.63 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 18 19 19 20 20 20 20 20 20 20 20 21 21 21 21 21 21 GDT PERCENT_AT 10.59 15.29 17.65 21.18 22.35 22.35 23.53 23.53 23.53 23.53 23.53 23.53 23.53 23.53 24.71 24.71 24.71 24.71 24.71 24.71 GDT RMS_LOCAL 0.28 0.56 0.80 1.16 1.30 1.30 1.58 1.58 1.58 1.58 1.58 1.58 1.58 1.58 2.54 2.54 2.54 2.54 2.54 2.54 GDT RMS_ALL_AT 2.99 3.01 2.82 3.09 3.00 3.00 2.73 2.73 2.73 2.73 2.73 2.73 2.73 2.73 2.54 2.54 2.54 2.54 2.54 2.54 # Checking swapping # 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 2.333 0 0.064 1.328 5.268 38.182 22.828 5.268 LGA Q 56 Q 56 1.621 0 0.021 0.211 3.000 58.182 48.687 1.531 LGA A 57 A 57 0.329 0 0.028 0.032 0.743 90.909 92.727 - LGA F 58 F 58 1.273 0 0.010 0.166 2.642 69.545 51.074 2.642 LGA D 59 D 59 1.526 0 0.068 0.150 2.333 58.182 49.773 2.333 LGA R 60 R 60 1.075 0 0.038 1.334 6.425 73.636 46.116 4.872 LGA L 61 L 61 0.456 0 0.026 0.099 1.067 95.455 86.591 0.946 LGA S 62 S 62 0.613 0 0.019 0.612 2.768 90.909 78.788 2.768 LGA E 63 E 63 0.176 0 0.058 0.142 0.668 100.000 97.980 0.342 LGA A 64 A 64 0.222 0 0.105 0.112 0.484 100.000 100.000 - LGA G 65 G 65 0.528 0 0.069 0.069 0.630 86.364 86.364 - LGA F 66 F 66 0.942 0 0.045 0.117 1.678 81.818 70.248 1.674 LGA H 67 H 67 0.901 0 0.148 0.171 1.261 81.818 72.000 1.260 LGA M 68 M 68 1.018 0 0.114 1.242 5.054 69.545 46.591 3.554 LGA V 69 V 69 0.578 0 0.039 0.062 1.471 73.636 70.130 1.471 LGA A 70 A 70 2.560 0 0.014 0.021 3.344 45.455 40.000 - LGA C 71 C 71 2.470 0 0.055 0.728 3.738 27.727 24.848 3.738 LGA N 72 N 72 2.225 0 0.104 0.947 4.539 51.818 32.500 4.539 LGA S 73 S 73 1.130 0 0.620 0.575 4.311 43.636 43.939 2.276 LGA S 74 S 74 3.686 0 0.092 0.132 6.632 12.273 11.515 4.565 LGA G 75 G 75 10.353 0 0.555 0.555 12.654 0.000 0.000 - # 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): 2.542 2.683 2.711 15.872 13.796 35.795 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 21 85 4.0 20 1.58 21.176 21.979 1.192 LGA_LOCAL RMSD: 1.577 Number of atoms: 20 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 2.734 Number of assigned atoms: 21 Std_ASGN_ATOMS RMSD: 2.542 Standard rmsd on all 21 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.869304 * X + -0.183835 * Y + -0.458819 * Z + 43.493198 Y_new = -0.454136 * X + 0.069375 * Y + -0.888227 * Z + 68.439018 Z_new = 0.195118 * X + 0.980506 * Y + -0.023179 * Z + 38.266033 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -0.481417 -0.196378 1.594431 [DEG: -27.5832 -11.2516 91.3542 ] ZXZ: -0.476805 1.593977 0.196431 [DEG: -27.3189 91.3282 11.2547 ] # 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_3 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_3.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 21 85 4.0 20 1.58 21.979 2.54 REMARK ---------------------------------------------------------- MOLECULE T0970TS347_3 PFRMAT TS TARGET T0970 MODEL 3 PARENT 1wpl_R 1jg5_B ATOM 1 N GLU 55 64.015 38.020 95.066 1.00 2.98 ATOM 0 CA GLU 55 65.365 38.611 94.964 1.00 2.98 ATOM 2 CB GLU 55 65.679 39.456 96.202 1.00 2.98 ATOM 3 C GLU 55 66.417 37.520 94.804 1.00 2.98 ATOM 4 O GLU 55 67.286 37.609 93.934 1.00 2.98 ATOM 5 CG GLU 55 67.158 39.490 96.563 1.00 2.98 ATOM 6 CD GLU 55 67.511 40.603 97.534 1.00 2.98 ATOM 7 OE1 GLU 55 66.663 40.941 98.390 1.00 2.98 ATOM 8 OE2 GLU 55 68.635 41.145 97.441 1.00 2.98 ATOM 10 N GLN 56 66.357 36.496 95.651 1.00 2.28 ATOM 9 CA GLN 56 67.297 35.385 95.551 1.00 2.28 ATOM 12 CB GLN 56 67.055 34.377 96.678 1.00 2.28 ATOM 13 C GLN 56 67.150 34.695 94.200 1.00 2.28 ATOM 14 O GLN 56 68.141 34.287 93.591 1.00 2.28 ATOM 15 CG GLN 56 67.348 34.927 98.066 1.00 2.28 ATOM 16 CD GLN 56 67.188 33.882 99.154 1.00 2.28 ATOM 17 NE2 GLN 56 68.037 33.946 100.174 1.00 2.28 ATOM 20 OE1 GLN 56 66.309 33.017 99.077 1.00 2.28 ATOM 22 N ALA 57 65.910 34.551 93.741 1.00 2.17 ATOM 21 CA ALA 57 65.655 33.950 92.437 1.00 2.17 ATOM 24 CB ALA 57 64.155 33.880 92.172 1.00 2.17 ATOM 25 C ALA 57 66.340 34.780 91.356 1.00 2.17 ATOM 26 O ALA 57 66.907 34.236 90.406 1.00 2.17 ATOM 28 N PHE 58 66.307 36.100 91.518 1.00 1.51 ATOM 27 CA PHE 58 66.954 36.999 90.570 1.00 1.51 ATOM 30 CB PHE 58 66.545 38.454 90.837 1.00 1.51 ATOM 31 C PHE 58 68.470 36.858 90.644 1.00 1.51 ATOM 32 O PHE 58 69.152 36.894 89.616 1.00 1.51 ATOM 33 CG PHE 58 65.065 38.695 90.698 1.00 1.51 ATOM 34 CD1 PHE 58 64.476 39.786 91.328 1.00 1.51 ATOM 35 CE1 PHE 58 63.108 40.012 91.192 1.00 1.51 ATOM 36 CZ PHE 58 62.335 39.154 90.421 1.00 1.51 ATOM 37 CD2 PHE 58 64.284 37.816 89.956 1.00 1.51 ATOM 38 CE2 PHE 58 62.916 38.043 89.823 1.00 1.51 ATOM 40 N ASP 59 68.995 36.674 91.849 1.00 1.23 ATOM 39 CA ASP 59 70.432 36.487 92.027 1.00 1.23 ATOM 42 CB ASP 59 70.788 36.436 93.516 1.00 1.23 ATOM 43 C ASP 59 70.894 35.212 91.329 1.00 1.23 ATOM 44 O ASP 59 71.891 35.222 90.603 1.00 1.23 ATOM 45 CG ASP 59 70.790 37.805 94.169 1.00 1.23 ATOM 46 OD1 ASP 59 70.713 38.817 93.440 1.00 1.23 ATOM 47 OD2 ASP 59 70.877 37.877 95.413 1.00 1.23 ATOM 49 N ARG 60 70.168 34.117 91.531 1.00 1.40 ATOM 48 CA ARG 60 70.498 32.856 90.877 1.00 1.40 ATOM 51 CB ARG 60 69.587 31.728 91.370 1.00 1.40 ATOM 52 C ARG 60 70.359 33.001 89.366 1.00 1.40 ATOM 53 O ARG 60 71.229 32.563 88.609 1.00 1.40 ATOM 54 CG ARG 60 68.967 30.913 90.246 1.00 1.40 ATOM 55 CD ARG 60 67.996 29.868 90.780 1.00 1.40 ATOM 56 NE ARG 60 66.629 30.126 90.334 1.00 1.40 ATOM 58 CZ ARG 60 66.154 29.826 89.128 1.00 1.40 ATOM 59 NH1 ARG 60 64.891 30.104 88.824 1.00 1.40 ATOM 60 NH2 ARG 60 66.935 29.238 88.228 1.00 1.40 ATOM 62 N LEU 61 69.268 33.621 88.926 1.00 1.10 ATOM 61 CA LEU 61 69.052 33.856 87.504 1.00 1.10 ATOM 64 CB LEU 61 67.787 34.694 87.289 1.00 1.10 ATOM 65 C LEU 61 70.257 34.582 86.916 1.00 1.10 ATOM 66 O LEU 61 70.689 34.286 85.800 1.00 1.10 ATOM 67 CG LEU 61 66.460 33.930 87.313 1.00 1.10 ATOM 68 CD1 LEU 61 65.293 34.907 87.242 1.00 1.10 ATOM 69 CD2 LEU 61 66.404 32.944 86.155 1.00 1.10 ATOM 71 N SER 62 70.812 35.520 87.678 1.00 1.31 ATOM 70 CA SER 62 71.995 36.251 87.238 1.00 1.31 ATOM 73 CB SER 62 72.390 37.299 88.283 1.00 1.31 ATOM 74 C SER 62 73.159 35.294 87.010 1.00 1.31 ATOM 75 O SER 62 73.877 35.410 86.014 1.00 1.31 ATOM 76 OG SER 62 71.282 38.120 88.611 1.00 1.31 ATOM 78 N GLU 63 73.356 34.357 87.931 1.00 2.48 ATOM 77 CA GLU 63 74.420 33.371 87.777 1.00 2.48 ATOM 80 CB GLU 63 74.504 32.477 89.018 1.00 2.48 ATOM 81 C GLU 63 74.176 32.519 86.538 1.00 2.48 ATOM 82 O GLU 63 75.121 32.094 85.870 1.00 2.48 ATOM 83 CG GLU 63 74.988 33.200 90.265 1.00 2.48 ATOM 84 CD GLU 63 75.214 32.273 91.447 1.00 2.48 ATOM 85 OE1 GLU 63 74.891 31.069 91.334 1.00 2.48 ATOM 86 OE2 GLU 63 75.722 32.744 92.489 1.00 2.48 ATOM 88 N ALA 64 72.904 32.284 86.223 1.00 2.52 ATOM 87 CA ALA 64 72.542 31.510 85.040 1.00 2.52 ATOM 90 CB ALA 64 71.085 31.066 85.129 1.00 2.52 ATOM 91 C ALA 64 72.763 32.323 83.768 1.00 2.52 ATOM 92 O ALA 64 72.991 31.759 82.695 1.00 2.52 ATOM 94 N GLY 65 72.703 33.646 83.889 1.00 2.23 ATOM 93 CA GLY 65 72.882 34.516 82.739 1.00 2.23 ATOM 96 C GLY 65 71.640 35.320 82.401 1.00 2.23 ATOM 97 O GLY 65 71.650 36.125 81.467 1.00 2.23 ATOM 99 N PHE 66 70.569 35.119 83.163 1.00 1.35 ATOM 98 CA PHE 66 69.327 35.854 82.949 1.00 1.35 ATOM 101 CB PHE 66 68.187 35.222 83.759 1.00 1.35 ATOM 102 C PHE 66 69.496 37.316 83.346 1.00 1.35 ATOM 103 O PHE 66 70.156 37.621 84.343 1.00 1.35 ATOM 104 CG PHE 66 67.807 33.842 83.289 1.00 1.35 ATOM 105 CD1 PHE 66 68.505 32.733 83.753 1.00 1.35 ATOM 106 CE1 PHE 66 68.167 31.459 83.302 1.00 1.35 ATOM 107 CZ PHE 66 67.125 31.297 82.397 1.00 1.35 ATOM 108 CD2 PHE 66 66.751 33.676 82.401 1.00 1.35 ATOM 109 CE2 PHE 66 66.406 32.401 81.959 1.00 1.35 ATOM 111 N HIS 67 68.917 38.219 82.562 1.00 1.37 ATOM 110 CA HIS 67 69.031 39.648 82.835 1.00 1.37 ATOM 113 CB HIS 67 69.793 40.349 81.703 1.00 1.37 ATOM 114 C HIS 67 67.657 40.286 83.003 1.00 1.37 ATOM 115 O HIS 67 66.897 40.401 82.040 1.00 1.37 ATOM 116 CG HIS 67 71.180 39.817 81.514 1.00 1.37 ATOM 117 ND1 HIS 67 72.212 40.123 82.373 1.00 1.37 ATOM 119 CE1 HIS 67 73.281 39.487 81.922 1.00 1.37 ATOM 120 NE2 HIS 67 72.995 38.816 80.818 1.00 1.37 ATOM 122 CD2 HIS 67 71.664 39.004 80.542 1.00 1.37 ATOM 124 N MET 68 67.339 40.719 84.220 1.00 2.49 ATOM 123 CA MET 68 66.056 41.360 84.487 1.00 2.49 ATOM 126 CB MET 68 65.945 41.738 85.968 1.00 2.49 ATOM 127 C MET 68 65.884 42.605 83.625 1.00 2.49 ATOM 128 O MET 68 66.438 43.662 83.934 1.00 2.49 ATOM 129 CG MET 68 66.022 40.551 86.916 1.00 2.49 ATOM 130 SD MET 68 64.628 39.416 86.714 1.00 2.49 ATOM 131 CE MET 68 63.282 40.435 87.296 1.00 2.49 ATOM 133 N VAL 69 65.110 42.485 82.552 1.00 3.57 ATOM 132 CA VAL 69 64.894 43.607 81.645 1.00 3.57 ATOM 135 CB VAL 69 63.966 43.210 80.473 1.00 3.57 ATOM 136 C VAL 69 64.289 44.779 82.411 1.00 3.57 ATOM 137 O VAL 69 64.723 45.923 82.254 1.00 3.57 ATOM 138 CG1 VAL 69 63.538 44.447 79.690 1.00 3.57 ATOM 139 CG2 VAL 69 64.667 42.220 79.550 1.00 3.57 ATOM 141 N ALA 70 63.285 44.498 83.237 1.00 2.99 ATOM 140 CA ALA 70 62.641 45.538 84.034 1.00 2.99 ATOM 143 CB ALA 70 61.786 46.433 83.141 1.00 2.99 ATOM 144 C ALA 70 61.783 44.928 85.138 1.00 2.99 ATOM 145 O ALA 70 61.285 43.809 84.997 1.00 2.99 ATOM 147 N CYS 71 61.604 45.663 86.232 1.00 2.78 ATOM 146 CA CYS 71 60.782 45.191 87.340 1.00 2.78 ATOM 149 CB CYS 71 61.586 45.196 88.643 1.00 2.78 ATOM 150 C CYS 71 59.532 46.048 87.498 1.00 2.78 ATOM 151 O CYS 71 59.614 47.203 87.923 1.00 2.78 ATOM 152 SG CYS 71 62.834 43.888 88.736 1.00 2.78 ATOM 154 N ASN 72 58.377 45.487 87.148 1.00 2.29 ATOM 153 CA ASN 72 57.116 46.217 87.229 1.00 2.29 ATOM 156 CB ASN 72 56.472 46.322 85.843 1.00 2.29 ATOM 157 C ASN 72 56.150 45.553 88.204 1.00 2.29 ATOM 158 O ASN 72 55.920 44.344 88.133 1.00 2.29 ATOM 159 CG ASN 72 55.244 47.213 85.835 1.00 2.29 ATOM 160 ND2 ASN 72 54.758 47.547 84.645 1.00 2.29 ATOM 163 OD1 ASN 72 54.741 47.605 86.891 1.00 2.29 ATOM 165 N SER 73 55.575 46.343 89.105 1.00 3.22 ATOM 164 CA SER 73 54.642 45.814 90.094 1.00 3.22 ATOM 167 CB SER 73 54.092 46.946 90.966 1.00 3.22 ATOM 168 C SER 73 53.486 45.075 89.428 1.00 3.22 ATOM 169 O SER 73 53.042 44.035 89.922 1.00 3.22 ATOM 170 OG SER 73 53.134 46.449 91.884 1.00 3.22 ATOM 172 N SER 74 53.001 45.601 88.308 1.00 4.41 ATOM 171 CA SER 74 51.879 44.990 87.603 1.00 4.41 ATOM 174 CB SER 74 51.217 46.010 86.674 1.00 4.41 ATOM 175 C SER 74 52.325 43.775 86.796 1.00 4.41 ATOM 176 O SER 74 53.521 43.581 86.568 1.00 4.41 ATOM 177 OG SER 74 52.039 46.267 85.547 1.00 4.41 ATOM 179 N GLY 75 51.366 42.967 86.357 1.00 8.17 ATOM 178 CA GLY 75 51.679 41.791 85.563 1.00 8.17 ATOM 181 C GLY 75 52.013 40.581 86.425 1.00 8.17 ATOM 182 O GLY 75 51.350 39.535 86.270 1.00 8.17 ATOM 183 OXT GLY 75 52.932 40.680 87.262 1.00 8.17 TER END