####################################################### # # # 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_2 # Molecule2: number of CA atoms 85 ( 650), selected 21 , name T0970.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0970TS347_2.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 20 55 - 74 4.91 5.64 LCS_AVERAGE: 23.36 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 16 55 - 70 1.74 9.75 LCS_AVERAGE: 16.13 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 15 55 - 69 0.98 10.78 LCS_AVERAGE: 13.84 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 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT Q 56 Q 56 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT A 57 A 57 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT F 58 F 58 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT D 59 D 59 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT R 60 R 60 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT L 61 L 61 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT S 62 S 62 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT E 63 E 63 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT A 64 A 64 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT G 65 G 65 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT F 66 F 66 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT H 67 H 67 15 16 20 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT M 68 M 68 15 16 20 3 3 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT V 69 V 69 15 16 20 3 4 5 14 15 15 15 16 16 17 17 17 17 18 18 19 19 20 20 21 LCS_GDT A 70 A 70 4 16 20 3 4 5 6 7 13 15 16 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT C 71 C 71 4 7 20 3 4 5 10 13 14 15 15 16 17 17 17 18 18 18 19 19 20 20 21 LCS_GDT N 72 N 72 4 7 20 3 4 5 5 7 9 13 14 15 15 16 17 18 18 18 19 19 20 20 21 LCS_GDT S 73 S 73 4 7 20 3 4 5 5 7 9 10 11 12 13 15 16 18 18 18 19 19 20 20 21 LCS_GDT S 74 S 74 3 7 20 3 3 5 5 7 9 10 11 12 13 13 14 15 17 18 19 19 20 20 21 LCS_GDT G 75 G 75 3 4 17 3 3 3 3 3 5 6 6 12 12 13 14 15 15 16 17 18 18 20 21 LCS_AVERAGE LCS_A: 17.78 ( 13.84 16.13 23.36 ) 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 13 13 14 14 15 15 15 16 16 17 17 17 18 18 18 19 19 20 20 21 GDT PERCENT_AT 15.29 15.29 16.47 16.47 17.65 17.65 17.65 18.82 18.82 20.00 20.00 20.00 21.18 21.18 21.18 22.35 22.35 23.53 23.53 24.71 GDT RMS_LOCAL 0.26 0.26 0.47 0.47 0.98 0.98 0.98 1.74 1.74 2.31 2.31 2.31 3.82 3.31 3.31 4.15 4.15 4.91 4.91 5.46 GDT RMS_ALL_AT 10.94 10.94 10.89 10.89 10.78 10.78 10.78 9.75 9.75 8.63 8.63 8.63 6.07 7.31 7.31 6.27 6.27 5.64 5.64 5.46 # Checking swapping # possible swapping detected: F 58 F 58 # possible swapping detected: F 66 F 66 # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all Dist_at LGA E 55 E 55 1.513 0 0.571 1.391 4.846 52.273 31.717 2.589 LGA Q 56 Q 56 0.858 0 0.014 0.183 1.690 81.818 74.747 0.708 LGA A 57 A 57 0.413 0 0.024 0.028 0.683 95.455 92.727 - LGA F 58 F 58 0.981 0 0.038 0.131 2.712 81.818 55.537 2.712 LGA D 59 D 59 1.116 0 0.058 0.151 1.728 69.545 62.045 1.560 LGA R 60 R 60 0.942 0 0.025 1.265 6.624 77.727 43.802 5.665 LGA L 61 L 61 0.300 0 0.038 0.093 0.933 100.000 93.182 0.925 LGA S 62 S 62 0.586 0 0.020 0.644 3.203 86.364 74.242 3.203 LGA E 63 E 63 0.749 0 0.082 0.359 1.482 77.727 78.182 0.674 LGA A 64 A 64 0.597 0 0.008 0.008 0.714 81.818 81.818 - LGA G 65 G 65 0.491 0 0.087 0.087 0.491 100.000 100.000 - LGA F 66 F 66 1.147 0 0.085 1.408 5.488 69.545 48.760 5.123 LGA H 67 H 67 1.863 0 0.108 0.141 2.725 50.909 40.000 2.581 LGA M 68 M 68 2.253 0 0.144 1.095 5.708 38.182 26.136 2.790 LGA V 69 V 69 2.786 0 0.579 0.558 5.607 23.636 13.766 5.487 LGA A 70 A 70 4.764 0 0.020 0.030 7.590 7.273 5.818 - LGA C 71 C 71 7.804 0 0.152 0.877 10.385 0.000 0.000 7.192 LGA N 72 N 72 14.468 0 0.116 0.225 17.294 0.000 0.000 12.875 LGA S 73 S 73 19.321 0 0.595 0.562 21.590 0.000 0.000 21.590 LGA S 74 S 74 24.480 0 0.063 0.107 26.385 0.000 0.000 26.385 LGA G 75 G 75 26.576 0 0.644 0.644 26.576 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): 5.461 5.324 5.618 12.872 10.853 26.477 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 21 85 4.0 16 1.74 18.235 17.811 0.872 LGA_LOCAL RMSD: 1.736 Number of atoms: 16 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 9.752 Number of assigned atoms: 21 Std_ASGN_ATOMS RMSD: 5.461 Standard rmsd on all 21 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = -0.057803 * X + 0.188487 * Y + -0.980373 * Z + 20.505278 Y_new = -0.712124 * X + 0.680453 * Y + 0.172811 * Z + 69.946877 Z_new = 0.699671 * X + 0.708136 * Y + 0.094894 * Z + 34.436539 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -1.651788 -0.774936 1.437584 [DEG: -94.6405 -44.4006 82.3675 ] ZXZ: -1.745275 1.475759 0.779385 [DEG: -99.9969 84.5548 44.6555 ] # 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_2 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_2.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 21 85 4.0 16 1.74 17.811 5.46 REMARK ---------------------------------------------------------- MOLECULE T0970TS347_2 PFRMAT TS TARGET T0970 MODEL 2 PARENT 1wpl_R 1jg5_B ATOM 1 N GLU 55 65.449 38.954 94.603 1.00 4.42 ATOM 0 CA GLU 55 65.518 37.902 95.635 1.00 4.42 ATOM 2 CB GLU 55 64.151 37.239 95.825 1.00 4.42 ATOM 3 C GLU 55 66.555 36.848 95.260 1.00 4.42 ATOM 4 O GLU 55 67.379 37.063 94.368 1.00 4.42 ATOM 5 CG GLU 55 63.132 38.126 96.524 1.00 4.42 ATOM 6 CD GLU 55 63.456 38.367 97.988 1.00 4.42 ATOM 7 OE1 GLU 55 64.547 37.951 98.435 1.00 4.42 ATOM 8 OE2 GLU 55 62.616 38.967 98.696 1.00 4.42 ATOM 10 N GLN 56 66.512 35.702 95.932 1.00 3.97 ATOM 9 CA GLN 56 67.449 34.622 95.643 1.00 3.97 ATOM 12 CB GLN 56 67.248 33.467 96.627 1.00 3.97 ATOM 13 C GLN 56 67.269 34.119 94.215 1.00 3.97 ATOM 14 O GLN 56 68.251 33.876 93.510 1.00 3.97 ATOM 15 CG GLN 56 67.418 33.869 98.085 1.00 3.97 ATOM 16 CD GLN 56 67.187 32.712 99.041 1.00 3.97 ATOM 17 NE2 GLN 56 68.005 32.629 100.084 1.00 3.97 ATOM 20 OE1 GLN 56 66.278 31.900 98.844 1.00 3.97 ATOM 22 N ALA 57 66.020 33.972 93.786 1.00 4.04 ATOM 21 CA ALA 57 65.740 33.533 92.423 1.00 4.04 ATOM 24 CB ALA 57 64.234 33.500 92.177 1.00 4.04 ATOM 25 C ALA 57 66.409 34.471 91.425 1.00 4.04 ATOM 26 O ALA 57 66.944 34.031 90.404 1.00 4.04 ATOM 28 N PHE 58 66.402 35.764 91.734 1.00 2.38 ATOM 27 CA PHE 58 67.031 36.758 90.872 1.00 2.38 ATOM 30 CB PHE 58 66.577 38.172 91.254 1.00 2.38 ATOM 31 C PHE 58 68.551 36.650 90.937 1.00 2.38 ATOM 32 O PHE 58 69.234 36.860 89.932 1.00 2.38 ATOM 33 CG PHE 58 65.116 38.421 90.984 1.00 2.38 ATOM 34 CD1 PHE 58 64.409 39.329 91.765 1.00 2.38 ATOM 35 CE1 PHE 58 63.058 39.559 91.513 1.00 2.38 ATOM 36 CZ PHE 58 62.422 38.893 90.474 1.00 2.38 ATOM 37 CD2 PHE 58 64.469 37.731 89.965 1.00 2.38 ATOM 38 CE2 PHE 58 63.120 37.965 89.712 1.00 2.38 ATOM 40 N ASP 59 69.080 36.304 92.105 1.00 1.49 ATOM 39 CA ASP 59 70.521 36.130 92.250 1.00 1.49 ATOM 42 CB ASP 59 70.902 35.936 93.722 1.00 1.49 ATOM 43 C ASP 59 70.992 34.941 91.418 1.00 1.49 ATOM 44 O ASP 59 72.003 35.025 90.719 1.00 1.49 ATOM 45 CG ASP 59 70.863 37.228 94.515 1.00 1.49 ATOM 46 OD1 ASP 59 70.720 38.308 93.900 1.00 1.49 ATOM 47 OD2 ASP 59 70.987 37.174 95.758 1.00 1.49 ATOM 49 N ARG 60 70.249 33.840 91.473 1.00 2.71 ATOM 48 CA ARG 60 70.583 32.658 90.685 1.00 2.71 ATOM 51 CB ARG 60 69.669 31.482 91.041 1.00 2.71 ATOM 52 C ARG 60 70.465 32.971 89.198 1.00 2.71 ATOM 53 O ARG 60 71.310 32.563 88.399 1.00 2.71 ATOM 54 CG ARG 60 68.578 31.225 90.013 1.00 2.71 ATOM 55 CD ARG 60 67.911 29.873 90.227 1.00 2.71 ATOM 56 NE ARG 60 66.470 29.935 89.995 1.00 2.71 ATOM 58 CZ ARG 60 65.891 29.882 88.798 1.00 2.71 ATOM 59 NH1 ARG 60 64.568 29.947 88.693 1.00 2.71 ATOM 60 NH2 ARG 60 66.633 29.773 87.701 1.00 2.71 ATOM 62 N LEU 61 69.422 33.712 88.830 1.00 1.23 ATOM 61 CA LEU 61 69.218 34.107 87.440 1.00 1.23 ATOM 64 CB LEU 61 67.899 34.873 87.298 1.00 1.23 ATOM 65 C LEU 61 70.379 34.966 86.955 1.00 1.23 ATOM 66 O LEU 61 70.874 34.780 85.841 1.00 1.23 ATOM 67 CG LEU 61 66.631 34.019 87.196 1.00 1.23 ATOM 68 CD1 LEU 61 65.393 34.903 87.277 1.00 1.23 ATOM 69 CD2 LEU 61 66.636 33.222 85.899 1.00 1.23 ATOM 71 N SER 62 70.826 35.894 87.796 1.00 2.37 ATOM 70 CA SER 62 71.958 36.746 87.451 1.00 2.37 ATOM 73 CB SER 62 72.214 37.767 88.563 1.00 2.37 ATOM 74 C SER 62 73.211 35.908 87.225 1.00 2.37 ATOM 75 O SER 62 73.953 36.133 86.266 1.00 2.37 ATOM 76 OG SER 62 71.144 38.693 88.647 1.00 2.37 ATOM 78 N GLU 63 73.436 34.930 88.096 1.00 3.85 ATOM 77 CA GLU 63 74.588 34.046 87.955 1.00 3.85 ATOM 80 CB GLU 63 74.690 33.104 89.159 1.00 3.85 ATOM 81 C GLU 63 74.492 33.233 86.670 1.00 3.85 ATOM 82 O GLU 63 75.498 33.006 85.994 1.00 3.85 ATOM 83 CG GLU 63 75.137 33.789 90.442 1.00 3.85 ATOM 84 CD GLU 63 75.227 32.841 91.625 1.00 3.85 ATOM 85 OE1 GLU 63 74.503 31.819 91.628 1.00 3.85 ATOM 86 OE2 GLU 63 76.026 33.109 92.548 1.00 3.85 ATOM 88 N ALA 64 73.280 32.808 86.323 1.00 3.78 ATOM 87 CA ALA 64 73.062 32.040 85.101 1.00 3.78 ATOM 90 CB ALA 64 71.664 31.428 85.107 1.00 3.78 ATOM 91 C ALA 64 73.246 32.914 83.865 1.00 3.78 ATOM 92 O ALA 64 73.235 32.415 82.737 1.00 3.78 ATOM 94 N GLY 65 73.424 34.214 84.074 1.00 3.97 ATOM 93 CA GLY 65 73.580 35.141 82.965 1.00 3.97 ATOM 96 C GLY 65 72.250 35.622 82.415 1.00 3.97 ATOM 97 O GLY 65 72.209 36.484 81.534 1.00 3.97 ATOM 99 N PHE 66 71.158 35.074 82.939 1.00 2.13 ATOM 98 CA PHE 66 69.820 35.468 82.511 1.00 2.13 ATOM 101 CB PHE 66 68.761 34.602 83.206 1.00 2.13 ATOM 102 C PHE 66 69.570 36.939 82.823 1.00 2.13 ATOM 103 O PHE 66 69.829 37.396 83.939 1.00 2.13 ATOM 104 CG PHE 66 67.400 35.243 83.282 1.00 2.13 ATOM 105 CD1 PHE 66 66.439 34.953 82.319 1.00 2.13 ATOM 106 CE1 PHE 66 65.176 35.535 82.399 1.00 2.13 ATOM 107 CZ PHE 66 64.875 36.401 83.443 1.00 2.13 ATOM 108 CD2 PHE 66 67.100 36.118 84.320 1.00 2.13 ATOM 109 CE2 PHE 66 65.835 36.693 84.403 1.00 2.13 ATOM 111 N HIS 67 69.082 37.681 81.834 1.00 4.08 ATOM 110 CA HIS 67 68.784 39.098 82.020 1.00 4.08 ATOM 113 CB HIS 67 69.074 39.877 80.731 1.00 4.08 ATOM 114 C HIS 67 67.332 39.300 82.431 1.00 4.08 ATOM 115 O HIS 67 66.414 38.929 81.697 1.00 4.08 ATOM 116 CG HIS 67 70.509 39.798 80.308 1.00 4.08 ATOM 117 ND1 HIS 67 71.509 40.481 80.962 1.00 4.08 ATOM 119 CE1 HIS 67 72.639 40.182 80.341 1.00 4.08 ATOM 120 NE2 HIS 67 72.417 39.342 79.344 1.00 4.08 ATOM 122 CD2 HIS 67 71.070 39.078 79.305 1.00 4.08 ATOM 124 N MET 68 67.115 39.872 83.612 1.00 4.81 ATOM 123 CA MET 68 65.763 40.130 84.097 1.00 4.81 ATOM 126 CB MET 68 65.731 40.084 85.627 1.00 4.81 ATOM 127 C MET 68 65.264 41.488 83.616 1.00 4.81 ATOM 128 O MET 68 66.058 42.348 83.232 1.00 4.81 ATOM 129 CG MET 68 66.858 39.266 86.240 1.00 4.81 ATOM 130 SD MET 68 66.732 39.156 88.040 1.00 4.81 ATOM 131 CE MET 68 66.796 40.885 88.484 1.00 4.81 ATOM 133 N VAL 69 63.949 41.684 83.645 1.00 8.02 ATOM 132 CA VAL 69 63.365 42.955 83.231 1.00 8.02 ATOM 135 CB VAL 69 61.824 42.930 83.345 1.00 8.02 ATOM 136 C VAL 69 63.931 44.081 84.092 1.00 8.02 ATOM 137 O VAL 69 63.649 44.155 85.290 1.00 8.02 ATOM 138 CG1 VAL 69 61.251 44.329 83.141 1.00 8.02 ATOM 139 CG2 VAL 69 61.229 41.962 82.328 1.00 8.02 ATOM 141 N ALA 70 64.740 44.947 83.488 1.00 6.40 ATOM 140 CA ALA 70 65.355 46.050 84.221 1.00 6.40 ATOM 143 CB ALA 70 66.702 45.616 84.791 1.00 6.40 ATOM 144 C ALA 70 65.536 47.269 83.323 1.00 6.40 ATOM 145 O ALA 70 65.704 47.135 82.108 1.00 6.40 ATOM 147 N CYS 71 65.514 48.459 83.918 1.00 3.84 ATOM 146 CA CYS 71 65.660 49.695 83.157 1.00 3.84 ATOM 149 CB CYS 71 65.504 50.907 84.079 1.00 3.84 ATOM 150 C CYS 71 67.014 49.752 82.460 1.00 3.84 ATOM 151 O CYS 71 67.971 49.110 82.898 1.00 3.84 ATOM 152 SG CYS 71 63.894 50.996 84.901 1.00 3.84 ATOM 154 N ASN 72 67.096 50.515 81.373 1.00 2.11 ATOM 153 CA ASN 72 68.343 50.655 80.628 1.00 2.11 ATOM 156 CB ASN 72 68.082 50.539 79.122 1.00 2.11 ATOM 157 C ASN 72 69.028 51.981 80.938 1.00 2.11 ATOM 158 O ASN 72 68.385 53.032 80.937 1.00 2.11 ATOM 159 CG ASN 72 67.520 49.184 78.732 1.00 2.11 ATOM 160 ND2 ASN 72 66.399 49.187 78.022 1.00 2.11 ATOM 163 OD1 ASN 72 68.082 48.142 79.080 1.00 2.11 ATOM 165 N SER 73 70.331 51.936 81.190 1.00 5.14 ATOM 164 CA SER 73 71.090 53.149 81.475 1.00 5.14 ATOM 167 CB SER 73 72.573 52.816 81.658 1.00 5.14 ATOM 168 C SER 73 70.931 54.168 80.352 1.00 5.14 ATOM 169 O SER 73 70.689 55.350 80.607 1.00 5.14 ATOM 170 OG SER 73 73.331 54.001 81.839 1.00 5.14 ATOM 172 N SER 74 71.060 53.712 79.109 1.00 7.92 ATOM 171 CA SER 74 70.914 54.594 77.957 1.00 7.92 ATOM 174 CB SER 74 71.880 54.178 76.843 1.00 7.92 ATOM 175 C SER 74 69.484 54.582 77.430 1.00 7.92 ATOM 176 O SER 74 68.738 53.630 77.668 1.00 7.92 ATOM 177 OG SER 74 71.668 52.824 76.479 1.00 7.92 ATOM 179 N GLY 75 69.100 55.641 76.725 1.00 7.13 ATOM 178 CA GLY 75 67.751 55.737 76.190 1.00 7.13 ATOM 181 C GLY 75 66.713 55.995 77.273 1.00 7.13 ATOM 182 O GLY 75 65.505 55.920 76.972 1.00 7.13 ATOM 183 OXT GLY 75 67.106 56.274 78.424 1.00 7.13 TER END