####################################################### # # # 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 20 ( 138), selected 20 , name T0989TS397_1-D2 # Molecule2: number of CA atoms 112 ( 843), selected 20 , name T0989-D2.pdb # PARAMETERS: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0989TS397_1-D2.lga # FIXED Atom-Atom correspondence # GDT and LCS analysis LCS - RMSD CUTOFF 5.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 20 135 - 154 4.45 4.45 LCS_AVERAGE: 17.86 LCS - RMSD CUTOFF 2.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 8 142 - 149 1.89 6.36 LCS_AVERAGE: 5.80 LCS - RMSD CUTOFF 1.00 length segment l_RMS g_RMS LONGEST_CONTINUOUS_SEGMENT: 5 142 - 146 0.81 10.65 LCS_AVERAGE: 3.71 LCS_GDT MOLECULE-1 MOLECULE-2 LCS_DETAILS GDT_DETAILS TOTAL NUMBER OF RESIDUE PAIRS: 20 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 A 135 A 135 3 6 20 0 3 4 5 6 7 7 9 11 12 16 16 17 19 20 20 20 20 20 20 LCS_GDT S 136 S 136 3 6 20 0 3 3 5 6 7 7 9 9 11 12 14 15 17 20 20 20 20 20 20 LCS_GDT S 137 S 137 4 6 20 3 3 4 5 6 7 7 9 11 14 16 16 18 19 20 20 20 20 20 20 LCS_GDT S 138 S 138 4 6 20 3 3 4 5 6 7 10 11 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT G 139 G 139 4 6 20 3 3 4 5 6 7 11 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT N 140 N 140 4 6 20 3 3 4 4 5 7 10 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT V 141 V 141 4 6 20 3 3 4 4 6 7 7 11 14 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT V 142 V 142 5 8 20 3 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT S 143 S 143 5 8 20 3 4 5 6 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT S 144 S 144 5 8 20 3 4 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT P 145 P 145 5 8 20 3 4 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT A 146 A 146 5 8 20 3 4 5 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT S 147 S 147 4 8 20 1 3 4 4 5 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT N 148 N 148 4 8 20 4 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT E 149 E 149 4 8 20 4 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT K 150 K 150 4 5 20 3 4 4 5 5 6 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT S 151 S 151 4 5 20 3 4 4 5 6 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT S 152 S 152 4 5 20 3 4 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT W 153 W 153 4 5 20 4 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_GDT V 154 V 154 4 4 20 4 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 LCS_AVERAGE LCS_A: 9.12 ( 3.71 5.80 17.86 ) 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 4 5 7 9 10 11 13 13 16 16 16 17 18 19 20 20 20 20 20 20 GDT PERCENT_AT 3.57 4.46 6.25 8.04 8.93 9.82 11.61 11.61 14.29 14.29 14.29 15.18 16.07 16.96 17.86 17.86 17.86 17.86 17.86 17.86 GDT RMS_LOCAL 0.30 0.59 1.04 1.30 1.49 1.73 2.29 2.29 3.23 3.20 3.20 3.47 3.81 4.17 4.45 4.45 4.45 4.45 4.45 4.45 GDT RMS_ALL_AT 5.07 5.43 5.13 5.40 5.47 5.56 5.71 5.71 4.80 4.85 4.85 4.77 4.66 4.50 4.45 4.45 4.45 4.45 4.45 4.45 # Checking swapping # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all Dist_at LGA A 135 A 135 6.456 0 0.089 0.117 10.475 0.000 0.000 - LGA S 136 S 136 8.559 0 0.695 0.688 10.766 0.000 0.303 4.669 LGA S 137 S 137 12.215 0 0.718 0.617 13.630 0.000 0.000 12.227 LGA S 138 S 138 12.157 0 0.030 0.104 12.157 0.000 0.000 9.873 LGA G 139 G 139 8.726 0 0.310 0.310 10.016 0.000 0.000 - LGA N 140 N 140 7.704 0 0.268 0.798 10.750 0.000 0.000 10.750 LGA V 141 V 141 6.154 0 0.613 0.517 9.557 1.364 0.779 9.557 LGA V 142 V 142 1.051 0 0.121 1.026 3.396 52.273 40.519 3.396 LGA S 143 S 143 2.225 0 0.597 0.849 4.087 34.545 25.758 3.725 LGA S 144 S 144 1.728 0 0.042 0.135 4.812 70.000 48.788 4.812 LGA P 145 P 145 1.608 0 0.477 0.448 5.034 48.182 29.870 5.034 LGA A 146 A 146 2.431 0 0.312 0.307 5.245 40.000 32.000 - LGA S 147 S 147 3.253 0 0.648 0.935 6.396 46.364 30.909 6.396 LGA N 148 N 148 1.056 0 0.594 0.513 4.194 43.636 52.727 1.562 LGA E 149 E 149 2.222 0 0.089 1.177 9.250 41.818 19.798 9.250 LGA K 150 K 150 4.396 0 0.655 1.193 12.692 19.545 8.687 12.692 LGA S 151 S 151 3.308 0 0.588 0.526 7.793 30.455 20.303 7.793 LGA S 152 S 152 0.754 0 0.117 0.165 2.310 77.727 69.091 2.310 LGA W 153 W 153 0.907 0 0.640 1.000 9.471 61.818 25.974 9.471 LGA V 154 V 154 1.441 0 0.536 0.525 4.156 51.364 36.623 3.107 # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all GDC_at NUMBER_OF_ATOMS_AA: 20 80 80 100.00 138 138 100.00 112 17 SUMMARY(RMSD_GDC): 4.454 4.414 5.488 5.528 3.948 8.235 #CA N1 N2 DIST N RMSD GDT_TS LGA_S3 LGA_Q SUMMARY(GDT) 20 112 4.0 13 2.29 10.491 9.823 0.545 LGA_LOCAL RMSD: 2.286 Number of atoms: 13 under DIST: 4.00 LGA_ASGN_ATOMS RMSD: 5.715 Number of assigned atoms: 20 Std_ASGN_ATOMS RMSD: 4.454 Standard rmsd on all 20 assigned CA atoms Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = 0.233505 * X + 0.289185 * Y + -0.928358 * Z + -21.053276 Y_new = -0.802843 * X + -0.481290 * Y + -0.351857 * Z + 126.526741 Z_new = -0.548561 * X + 0.827485 * Y + 0.119787 * Z + -72.856598 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -1.287758 0.580642 1.427035 [DEG: -73.7831 33.2683 81.7631 ] ZXZ: -1.208514 1.450721 -0.585408 [DEG: -69.2428 83.1202 -33.5414 ] # 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: T0989TS397_1-D2 REMARK 2: T0989-D2.pdb REMARK GDT and LCS analysis REMARK FIXED Atom-Atom correspondence REMARK LGA parameters: -3 -ie -o1 -sda -d:4 -gdc_sc -swap T0989TS397_1-D2.lga REMARK #CA N1 N2 DIST N RMSD LGA_S3 RMSD_global REMARK SUMMARY: 20 112 4.0 13 2.29 9.823 4.45 REMARK ---------------------------------------------------------- MOLECULE T0989TS397_1-D2 PFRMAT TS TARGET T0989 MODEL 1 PARENT 4uxf_A 4uxf_B 4uxf_C ATOM 1960 N ALA 135 -20.857 17.659 -59.532 1.00 66.52 ATOM 1962 CA ALA 135 -20.044 18.711 -58.902 1.00 66.52 ATOM 1964 CB ALA 135 -19.064 18.127 -57.868 1.00 66.52 ATOM 1968 C ALA 135 -19.282 19.447 -60.021 1.00 66.52 ATOM 1969 O ALA 135 -18.912 18.796 -60.988 1.00 66.52 ATOM 1970 N SER 136 -19.034 20.764 -59.909 1.00 47.03 ATOM 1972 CA SER 136 -18.244 21.527 -60.890 1.00 47.03 ATOM 1974 CB SER 136 -18.335 23.047 -60.638 1.00 47.03 ATOM 1977 OG SER 136 -18.181 23.442 -59.291 1.00 47.03 ATOM 1979 C SER 136 -16.791 21.060 -61.101 1.00 47.03 ATOM 1980 O SER 136 -16.204 21.342 -62.157 1.00 47.03 ATOM 1981 N SER 137 -16.223 20.314 -60.151 1.00 46.51 ATOM 1983 CA SER 137 -14.943 19.631 -60.246 1.00 46.51 ATOM 1985 CB SER 137 -13.793 20.637 -60.063 1.00 46.51 ATOM 1988 OG SER 137 -13.845 21.315 -58.816 1.00 46.51 ATOM 1990 C SER 137 -14.939 18.454 -59.252 1.00 46.51 ATOM 1991 O SER 137 -15.793 18.391 -58.374 1.00 46.51 ATOM 1992 N SER 138 -13.989 17.533 -59.431 1.00 64.25 ATOM 1994 CA SER 138 -13.461 16.594 -58.434 1.00 64.25 ATOM 1996 CB SER 138 -12.915 17.314 -57.178 1.00 64.25 ATOM 1999 OG SER 138 -13.871 17.749 -56.216 1.00 64.25 ATOM 2001 C SER 138 -14.323 15.354 -58.153 1.00 64.25 ATOM 2002 O SER 138 -13.946 14.526 -57.328 1.00 64.25 ATOM 2003 N GLY 139 -15.456 15.210 -58.844 1.00 37.67 ATOM 2005 CA GLY 139 -16.557 14.381 -58.373 1.00 37.67 ATOM 2008 C GLY 139 -16.655 13.037 -59.072 1.00 37.67 ATOM 2009 O GLY 139 -16.735 12.971 -60.303 1.00 37.67 ATOM 2010 N ASN 140 -16.761 11.966 -58.280 1.00 28.76 ATOM 2012 CA ASN 140 -17.372 10.692 -58.662 1.00 28.76 ATOM 2014 CB ASN 140 -16.634 9.470 -58.036 1.00 28.76 ATOM 2017 CG ASN 140 -15.101 9.553 -58.016 1.00 28.76 ATOM 2018 OD1 ASN 140 -14.449 9.730 -59.035 1.00 28.76 ATOM 2019 ND2 ASN 140 -14.486 9.381 -56.845 1.00 28.76 ATOM 2022 C ASN 140 -18.749 10.830 -57.992 1.00 28.76 ATOM 2023 O ASN 140 -18.832 10.814 -56.764 1.00 28.76 ATOM 2024 N VAL 141 -19.782 11.267 -58.706 1.00 53.41 ATOM 2026 CA VAL 141 -20.725 10.385 -59.421 1.00 53.41 ATOM 2028 CB VAL 141 -22.138 10.584 -58.764 1.00 53.41 ATOM 2030 CG1 VAL 141 -23.248 9.648 -59.271 1.00 53.41 ATOM 2034 CG2 VAL 141 -22.128 10.485 -57.230 1.00 53.41 ATOM 2038 C VAL 141 -20.729 10.733 -60.934 1.00 53.41 ATOM 2039 O VAL 141 -21.438 10.118 -61.721 1.00 53.41 ATOM 2040 N VAL 142 -19.960 11.756 -61.321 1.00 45.96 ATOM 2042 CA VAL 142 -20.053 12.480 -62.583 1.00 45.96 ATOM 2044 CB VAL 142 -19.230 13.792 -62.458 1.00 45.96 ATOM 2046 CG1 VAL 142 -19.482 14.767 -63.628 1.00 45.96 ATOM 2050 CG2 VAL 142 -19.473 14.493 -61.108 1.00 45.96 ATOM 2054 C VAL 142 -19.559 11.631 -63.757 1.00 45.96 ATOM 2055 O VAL 142 -18.578 10.906 -63.627 1.00 45.96 ATOM 2056 N SER 143 -20.238 11.750 -64.913 1.00 97.09 ATOM 2058 CA SER 143 -19.837 11.190 -66.201 1.00 97.09 ATOM 2060 CB SER 143 -18.584 11.895 -66.772 1.00 97.09 ATOM 2063 OG SER 143 -17.449 11.951 -65.915 1.00 97.09 ATOM 2065 C SER 143 -19.892 9.639 -66.177 1.00 97.09 ATOM 2066 O SER 143 -18.994 8.978 -66.670 1.00 97.09 ATOM 2067 N SER 144 -20.934 9.114 -65.526 1.00 64.08 ATOM 2069 CA SER 144 -21.174 7.728 -65.112 1.00 64.08 ATOM 2071 CB SER 144 -22.506 7.732 -64.318 1.00 64.08 ATOM 2074 OG SER 144 -23.666 7.726 -65.149 1.00 64.08 ATOM 2076 C SER 144 -21.155 6.712 -66.278 1.00 64.08 ATOM 2077 O SER 144 -21.266 7.123 -67.438 1.00 64.08 ATOM 2078 N PRO 145 -21.092 5.384 -66.021 1.00 0.00 ATOM 2079 CA PRO 145 -20.981 4.388 -67.086 1.00 0.00 ATOM 2081 CB PRO 145 -20.495 3.120 -66.374 1.00 0.00 ATOM 2084 CG PRO 145 -21.056 3.226 -64.981 1.00 0.00 ATOM 2087 CD PRO 145 -21.075 4.732 -64.714 1.00 0.00 ATOM 2090 C PRO 145 -22.311 4.193 -67.859 1.00 0.00 ATOM 2091 O PRO 145 -23.146 3.378 -67.461 1.00 0.00 ATOM 2092 N ALA 146 -22.492 4.960 -68.932 1.00 71.35 ATOM 2094 CA ALA 146 -23.574 4.871 -69.899 1.00 71.35 ATOM 2096 CB ALA 146 -24.926 5.199 -69.224 1.00 71.35 ATOM 2100 C ALA 146 -23.310 5.857 -71.049 1.00 71.35 ATOM 2101 O ALA 146 -23.384 7.067 -70.827 1.00 71.35 ATOM 2102 N SER 147 -23.060 5.353 -72.264 1.00 44.74 ATOM 2104 CA SER 147 -23.270 6.079 -73.508 1.00 44.74 ATOM 2106 CB SER 147 -22.150 5.710 -74.513 1.00 44.74 ATOM 2109 OG SER 147 -22.287 4.404 -75.068 1.00 44.74 ATOM 2111 C SER 147 -24.639 5.633 -74.075 1.00 44.74 ATOM 2112 O SER 147 -25.118 4.532 -73.762 1.00 44.74 ATOM 2113 N ASN 148 -25.246 6.462 -74.927 1.00 40.71 ATOM 2115 CA ASN 148 -26.415 6.111 -75.750 1.00 40.71 ATOM 2117 CB ASN 148 -27.738 6.735 -75.239 1.00 40.71 ATOM 2120 CG ASN 148 -28.222 6.291 -73.866 1.00 40.71 ATOM 2121 OD1 ASN 148 -27.960 5.190 -73.401 1.00 40.71 ATOM 2122 ND2 ASN 148 -28.962 7.149 -73.157 1.00 40.71 ATOM 2125 C ASN 148 -26.201 6.526 -77.215 1.00 40.71 ATOM 2126 O ASN 148 -27.142 6.494 -78.005 1.00 40.71 ATOM 2127 N GLU 149 -25.004 6.997 -77.577 1.00 55.16 ATOM 2129 CA GLU 149 -24.734 7.639 -78.857 1.00 55.16 ATOM 2131 CB GLU 149 -23.841 8.871 -78.585 1.00 55.16 ATOM 2134 CG GLU 149 -24.670 9.998 -77.942 1.00 55.16 ATOM 2137 CD GLU 149 -24.074 11.398 -78.061 1.00 55.16 ATOM 2138 OE1 GLU 149 -23.214 11.645 -78.931 1.00 55.16 ATOM 2139 OE2 GLU 149 -24.500 12.256 -77.256 1.00 55.16 ATOM 2140 C GLU 149 -24.036 6.664 -79.813 1.00 55.16 ATOM 2141 O GLU 149 -23.559 5.594 -79.429 1.00 55.16 ATOM 2142 N LYS 150 -23.999 7.040 -81.094 1.00 43.88 ATOM 2144 CA LYS 150 -23.187 6.419 -82.137 1.00 43.88 ATOM 2146 CB LYS 150 -23.997 6.456 -83.464 1.00 43.88 ATOM 2149 CG LYS 150 -25.391 5.817 -83.288 1.00 43.88 ATOM 2152 CD LYS 150 -26.237 5.656 -84.560 1.00 43.88 ATOM 2155 CE LYS 150 -27.624 5.060 -84.205 1.00 43.88 ATOM 2158 NZ LYS 150 -28.515 4.911 -85.370 1.00 43.88 ATOM 2162 C LYS 150 -21.852 7.198 -82.271 1.00 43.88 ATOM 2163 O LYS 150 -20.898 6.675 -82.849 1.00 43.88 ATOM 2164 N SER 151 -21.784 8.394 -81.660 1.00 55.75 ATOM 2166 CA SER 151 -20.640 9.218 -81.303 1.00 55.75 ATOM 2168 CB SER 151 -19.471 8.438 -80.630 1.00 55.75 ATOM 2171 OG SER 151 -18.748 7.618 -81.529 1.00 55.75 ATOM 2173 C SER 151 -20.299 10.249 -82.393 1.00 55.75 ATOM 2174 O SER 151 -19.825 9.910 -83.481 1.00 55.75 ATOM 2175 N SER 152 -20.530 11.527 -82.101 1.00 56.88 ATOM 2177 CA SER 152 -20.300 12.668 -82.980 1.00 56.88 ATOM 2179 CB SER 152 -21.532 12.877 -83.902 1.00 56.88 ATOM 2182 OG SER 152 -22.753 12.935 -83.176 1.00 56.88 ATOM 2184 C SER 152 -19.858 13.864 -82.137 1.00 56.88 ATOM 2185 O SER 152 -20.361 14.065 -81.022 1.00 56.88 ATOM 2186 N TRP 153 -18.860 14.615 -82.629 1.00 38.96 ATOM 2188 CA TRP 153 -18.220 15.702 -81.906 1.00 38.96 ATOM 2190 CB TRP 153 -16.796 15.900 -82.482 1.00 38.96 ATOM 2193 CG TRP 153 -15.984 17.058 -81.971 1.00 38.96 ATOM 2194 CD1 TRP 153 -15.289 17.093 -80.816 1.00 38.96 ATOM 2196 CD2 TRP 153 -15.774 18.361 -82.604 1.00 38.96 ATOM 2197 NE1 TRP 153 -14.657 18.312 -80.690 1.00 38.96 ATOM 2199 CE2 TRP 153 -14.926 19.139 -81.759 1.00 38.96 ATOM 2200 CE3 TRP 153 -16.246 18.979 -83.783 1.00 38.96 ATOM 2202 CZ2 TRP 153 -14.575 20.470 -82.062 1.00 38.96 ATOM 2204 CZ3 TRP 153 -15.917 20.308 -84.092 1.00 38.96 ATOM 2206 CH2 TRP 153 -15.089 21.057 -83.233 1.00 38.96 ATOM 2208 C TRP 153 -19.046 16.991 -82.101 1.00 38.96 ATOM 2209 O TRP 153 -19.205 17.449 -83.240 1.00 38.96 ATOM 2210 N VAL 154 -19.508 17.566 -80.988 1.00 95.22 ATOM 2212 CA VAL 154 -20.136 18.876 -80.840 1.00 95.22 ATOM 2214 CB VAL 154 -19.267 20.035 -81.473 1.00 95.22 ATOM 2216 CG1 VAL 154 -19.956 21.387 -81.667 1.00 95.22 ATOM 2220 CG2 VAL 154 -17.964 20.247 -80.681 1.00 95.22 ATOM 2224 C VAL 154 -21.670 18.849 -81.033 1.00 95.22 ATOM 2225 O VAL 154 -22.261 17.796 -81.366 1.00 95.22 TER END