HEADER PLANT PROTEIN 08-MAY-05 1ZLO TITLE HOMOLOGY MODEL OF THE CYCLOTIDE VODO M COMPND MOL_ID: 1; COMPND 2 MOLECULE: VODO PEPTIDE M; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIOLA ODORATA; SOURCE 3 ORGANISM_COMMON: SWEET VIOLET KEYWDS CYCLIC, MACROCYCLIC, CYCLOTIDE, VIOLA ODORATA, VODO M, KEYWDS 2 CYCLIC CYSTEIN KNOT (CCK) MOTIF EXPDTA THEORETICAL MODEL AUTHOR E.SVANGARD,U.GORANSSON,D.SMITH,C.VERMA,A.BACKLUND,L.BOHLIN, AUTHOR 2 P.CLAESON REVDAT 1 17-MAY-05 1ZLO 0 JRNL AUTH E.SVANGARD,U.GORANSSON,D.SMITH,C.VERMA,A.BACKLUND, JRNL AUTH 2 L.BOHLIN,P.CLAESON JRNL TITL PRIMARY AND 3-D MODELLED STRUCTURES OF TWO JRNL TITL 2 CYCLOTIDES FROM VIOLA ODORATA JRNL REF PHYTOCHEMISTRY V. 64 135 2003 JRNL REFN ASTM PYTCAS US ISSN 0031-9422 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MODELLER 4 REMARK 3 AUTHORS : SALI, SANCHEZ, BADRETDINOV REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS PEPTIDE IS MACROCYCLIC I.E. THE REMARK 3 N- AND C-TERMINAL ARE JOINED WITH A PEPTIDE BOND AND HENCE THE REMARK 3 CLOSE CONTACT BETWEEN SER 1 AND CYS 29 REMARK 4 REMARK 4 1ZLO COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-2005. REMARK 100 THE RCSB ID CODE IS RCSB032864. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 N SER A 1 C CYS A 29 1.35 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 22 -54.34 77.27 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KAL RELATED DB: PDB REMARK 900 TEMPLATE STRUCTURE, MEMBER OF THE CYCLOTIDE FAMILY REMARK 900 RELATED ID: 1BH4 RELATED DB: PDB REMARK 900 MEMBER OF THE CYCLOTIDE FAMILY REMARK 900 RELATED ID: 1DF6 RELATED DB: PDB REMARK 900 MEMBER OF THE CYCLOTIDE FAMILY DBREF 1ZLO A 1 21 UNP P83839 VODM_VIOOD 9 29 DBREF 1ZLO A 22 29 UNP P83839 VODM_VIOOD 1 8 SEQRES 1 A 29 SER TRP PRO VAL CYS THR ARG ASN GLY ALA PRO ILE CYS SEQRES 2 A 29 GLY GLU SER CYS PHE THR GLY LYS CYS TYR THR VAL GLN SEQRES 3 A 29 CYS SER CYS SSBOND 1 CYS A 5 CYS A 22 SSBOND 2 CYS A 13 CYS A 27 SSBOND 3 CYS A 17 CYS A 29 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 N SER A 1 11.642 17.875 15.640 1.00106.03 N ATOM 2 CA SER A 1 10.344 17.306 15.818 1.00106.03 C ATOM 3 C SER A 1 10.525 15.969 15.199 1.00106.03 C ATOM 4 O SER A 1 11.623 15.686 14.732 1.00106.03 O ATOM 5 CB SER A 1 9.200 18.036 15.095 1.00106.03 C ATOM 6 OG SER A 1 9.345 17.922 13.690 1.00106.03 O ATOM 7 N TRP A 2 9.487 15.114 15.151 1.00 85.09 N ATOM 8 CA TRP A 2 9.751 13.795 14.654 1.00 85.09 C ATOM 9 C TRP A 2 10.257 13.841 13.238 1.00 85.09 C ATOM 10 O TRP A 2 11.329 13.297 12.981 1.00 85.09 O ATOM 11 CB TRP A 2 8.525 12.862 14.720 1.00 85.09 C ATOM 12 CG TRP A 2 8.792 11.484 14.163 1.00 85.09 C ATOM 13 CD1 TRP A 2 9.467 10.453 14.745 1.00 85.09 C ATOM 14 CD2 TRP A 2 8.364 11.007 12.875 1.00 85.09 C ATOM 15 NE1 TRP A 2 9.504 9.374 13.898 1.00 85.09 N ATOM 16 CE2 TRP A 2 8.827 9.700 12.747 1.00 85.09 C ATOM 17 CE3 TRP A 2 7.650 11.610 11.880 1.00 85.09 C ATOM 18 CZ2 TRP A 2 8.586 8.967 11.619 1.00 85.09 C ATOM 19 CZ3 TRP A 2 7.408 10.865 10.745 1.00 85.09 C ATOM 20 CH2 TRP A 2 7.866 9.570 10.616 1.00 85.09 C ATOM 21 N PRO A 3 9.563 14.430 12.294 1.00110.79 N ATOM 22 CA PRO A 3 10.009 14.484 10.926 1.00110.79 C ATOM 23 C PRO A 3 11.068 15.486 10.572 1.00110.79 C ATOM 24 O PRO A 3 11.810 15.221 9.629 1.00110.79 O ATOM 25 CB PRO A 3 8.749 14.717 10.092 1.00110.79 C ATOM 26 CG PRO A 3 7.763 15.378 11.073 1.00110.79 C ATOM 27 CD PRO A 3 8.159 14.781 12.430 1.00110.79 C ATOM 28 N VAL A 4 11.175 16.642 11.262 1.00120.34 N ATOM 29 CA VAL A 4 12.101 17.604 10.726 1.00120.34 C ATOM 30 C VAL A 4 12.847 18.302 11.830 1.00120.34 C ATOM 31 O VAL A 4 12.528 18.140 13.009 1.00120.34 O ATOM 32 CB VAL A 4 11.438 18.609 9.821 1.00120.34 C ATOM 33 CG1 VAL A 4 10.538 19.522 10.661 1.00120.34 C ATOM 34 CG2 VAL A 4 12.516 19.345 9.010 1.00120.34 C ATOM 35 N CYS A 5 13.901 19.064 11.451 1.00 61.87 N ATOM 36 CA CYS A 5 14.757 19.749 12.381 1.00 61.87 C ATOM 37 C CYS A 5 14.238 21.136 12.545 1.00 61.87 C ATOM 38 O CYS A 5 13.954 21.840 11.577 1.00 61.87 O ATOM 39 CB CYS A 5 16.235 19.775 11.936 1.00 61.87 C ATOM 40 SG CYS A 5 16.928 18.093 11.921 1.00 61.87 S ATOM 41 N THR A 6 14.122 21.566 13.811 1.00137.28 N ATOM 42 CA THR A 6 13.448 22.783 14.144 1.00137.28 C ATOM 43 C THR A 6 14.259 23.621 15.075 1.00137.28 C ATOM 44 O THR A 6 15.116 23.137 15.816 1.00137.28 O ATOM 45 CB THR A 6 12.163 22.446 14.832 1.00137.28 C ATOM 46 OG1 THR A 6 11.469 23.618 15.200 1.00137.28 O ATOM 47 CG2 THR A 6 12.478 21.591 16.072 1.00137.28 C ATOM 48 N ARG A 7 14.003 24.942 15.031 1.00141.65 N ATOM 49 CA ARG A 7 14.631 25.828 15.957 1.00141.65 C ATOM 50 C ARG A 7 13.523 26.350 16.801 1.00141.65 C ATOM 51 O ARG A 7 12.666 27.110 16.352 1.00141.65 O ATOM 52 CB ARG A 7 15.302 27.033 15.291 1.00141.65 C ATOM 53 CG ARG A 7 16.278 27.774 16.199 1.00141.65 C ATOM 54 CD ARG A 7 16.889 28.993 15.523 1.00141.65 C ATOM 55 NE ARG A 7 15.755 29.920 15.256 1.00141.65 N ATOM 56 CZ ARG A 7 15.934 31.269 15.265 1.00141.65 C ATOM 57 NH1 ARG A 7 17.185 31.804 15.393 1.00141.65 N ATOM 58 NH2 ARG A 7 14.855 32.096 15.162 1.00141.65 N ATOM 59 N ASN A 8 13.509 25.908 18.061 1.00 82.59 N ATOM 60 CA ASN A 8 12.535 26.334 19.015 1.00 82.59 C ATOM 61 C ASN A 8 11.140 26.234 18.459 1.00 82.59 C ATOM 62 O ASN A 8 10.305 27.101 18.720 1.00 82.59 O ATOM 63 CB ASN A 8 12.766 27.756 19.580 1.00 82.59 C ATOM 64 CG ASN A 8 12.613 28.823 18.499 1.00 82.59 C ATOM 65 OD1 ASN A 8 13.518 29.075 17.704 1.00 82.59 O ATOM 66 ND2 ASN A 8 11.428 29.495 18.487 1.00 82.59 N ATOM 67 N GLY A 9 10.834 25.160 17.699 1.00 37.18 N ATOM 68 CA GLY A 9 9.472 24.959 17.277 1.00 37.18 C ATOM 69 C GLY A 9 9.256 25.196 15.809 1.00 37.18 C ATOM 70 O GLY A 9 8.244 24.747 15.275 1.00 37.18 O ATOM 71 N ALA A 10 10.154 25.905 15.096 1.00 52.90 N ATOM 72 CA ALA A 10 9.886 26.062 13.692 1.00 52.90 C ATOM 73 C ALA A 10 10.944 25.340 12.909 1.00 52.90 C ATOM 74 O ALA A 10 12.132 25.545 13.153 1.00 52.90 O ATOM 75 CB ALA A 10 9.919 27.529 13.243 1.00 52.90 C ATOM 76 N PRO A 11 10.555 24.469 11.994 1.00113.03 N ATOM 77 CA PRO A 11 11.486 23.748 11.148 1.00113.03 C ATOM 78 C PRO A 11 12.331 24.707 10.346 1.00113.03 C ATOM 79 O PRO A 11 11.949 25.057 9.229 1.00113.03 O ATOM 80 CB PRO A 11 10.615 22.903 10.225 1.00113.03 C ATOM 81 CG PRO A 11 9.323 23.737 10.108 1.00113.03 C ATOM 82 CD PRO A 11 9.201 24.448 11.469 1.00113.03 C ATOM 83 N ILE A 12 13.452 25.157 10.933 1.00173.76 N ATOM 84 CA ILE A 12 14.450 26.056 10.419 1.00173.76 C ATOM 85 C ILE A 12 15.520 25.398 9.607 1.00173.76 C ATOM 86 O ILE A 12 16.084 26.016 8.717 1.00173.76 O ATOM 87 CB ILE A 12 15.226 26.756 11.510 1.00173.76 C ATOM 88 CG1 ILE A 12 16.037 25.734 12.338 1.00173.76 C ATOM 89 CG2 ILE A 12 14.256 27.611 12.339 1.00173.76 C ATOM 90 CD1 ILE A 12 17.187 26.356 13.132 1.00173.76 C ATOM 91 N CYS A 13 15.898 24.171 9.998 1.00 96.73 N ATOM 92 CA CYS A 13 17.151 23.560 9.642 1.00 96.73 C ATOM 93 C CYS A 13 17.298 23.251 8.178 1.00 96.73 C ATOM 94 O CYS A 13 18.295 23.641 7.568 1.00 96.73 O ATOM 95 CB CYS A 13 17.351 22.276 10.480 1.00 96.73 C ATOM 96 SG CYS A 13 19.055 22.016 11.057 1.00 96.73 S ATOM 97 N GLY A 14 16.296 22.585 7.566 1.00 32.90 N ATOM 98 CA GLY A 14 16.404 22.207 6.185 1.00 32.90 C ATOM 99 C GLY A 14 16.694 20.736 6.107 1.00 32.90 C ATOM 100 O GLY A 14 16.784 20.177 5.015 1.00 32.90 O ATOM 101 N GLU A 15 16.844 20.062 7.265 1.00 56.50 N ATOM 102 CA GLU A 15 17.122 18.652 7.302 1.00 56.50 C ATOM 103 C GLU A 15 15.972 17.984 8.004 1.00 56.50 C ATOM 104 O GLU A 15 15.151 18.673 8.611 1.00 56.50 O ATOM 105 CB GLU A 15 18.397 18.324 8.091 1.00 56.50 C ATOM 106 CG GLU A 15 18.722 16.833 8.114 1.00 56.50 C ATOM 107 CD GLU A 15 19.921 16.646 9.027 1.00 56.50 C ATOM 108 OE1 GLU A 15 21.030 17.127 8.675 1.00 56.50 O ATOM 109 OE2 GLU A 15 19.734 16.016 10.103 1.00 56.50 O ATOM 110 N SER A 16 15.874 16.630 7.916 1.00 71.80 N ATOM 111 CA SER A 16 14.779 15.881 8.493 1.00 71.80 C ATOM 112 C SER A 16 15.282 14.825 9.448 1.00 71.80 C ATOM 113 O SER A 16 16.372 14.280 9.287 1.00 71.80 O ATOM 114 CB SER A 16 13.913 15.158 7.448 1.00 71.80 C ATOM 115 OG SER A 16 14.680 14.168 6.777 1.00 71.80 O ATOM 116 N CYS A 17 14.527 14.652 10.550 1.00191.98 N ATOM 117 CA CYS A 17 14.616 13.793 11.710 1.00191.98 C ATOM 118 C CYS A 17 13.801 12.536 11.710 1.00191.98 C ATOM 119 O CYS A 17 13.533 12.061 12.811 1.00191.98 O ATOM 120 CB CYS A 17 14.364 14.597 13.007 1.00191.98 C ATOM 121 SG CYS A 17 14.970 13.774 14.509 1.00191.98 S ATOM 122 N PHE A 18 13.299 12.005 10.582 1.00 80.96 N ATOM 123 CA PHE A 18 12.328 10.931 10.595 1.00 80.96 C ATOM 124 C PHE A 18 12.725 9.818 11.535 1.00 80.96 C ATOM 125 O PHE A 18 11.871 9.313 12.264 1.00 80.96 O ATOM 126 CB PHE A 18 12.162 10.269 9.221 1.00 80.96 C ATOM 127 CG PHE A 18 11.552 11.266 8.304 1.00 80.96 C ATOM 128 CD1 PHE A 18 12.316 12.242 7.706 1.00 80.96 C ATOM 129 CD2 PHE A 18 10.206 11.211 8.039 1.00 80.96 C ATOM 130 CE1 PHE A 18 11.738 13.156 6.855 1.00 80.96 C ATOM 131 CE2 PHE A 18 9.623 12.120 7.191 1.00 80.96 C ATOM 132 CZ PHE A 18 10.390 13.095 6.598 1.00 80.96 C ATOM 133 N THR A 19 14.007 9.405 11.551 1.00122.94 N ATOM 134 CA THR A 19 14.457 8.361 12.437 1.00122.94 C ATOM 135 C THR A 19 14.435 8.819 13.868 1.00122.94 C ATOM 136 O THR A 19 14.247 8.013 14.775 1.00122.94 O ATOM 137 CB THR A 19 15.839 7.850 12.169 1.00122.94 C ATOM 138 OG1 THR A 19 16.793 8.884 12.337 1.00122.94 O ATOM 139 CG2 THR A 19 15.892 7.276 10.745 1.00122.94 C ATOM 140 N GLY A 20 14.637 10.125 14.117 1.00 65.50 N ATOM 141 CA GLY A 20 14.646 10.651 15.453 1.00 65.50 C ATOM 142 C GLY A 20 16.004 11.216 15.757 1.00 65.50 C ATOM 143 O GLY A 20 16.311 11.468 16.924 1.00 65.50 O ATOM 144 N LYS A 21 16.902 11.272 14.743 1.00132.93 N ATOM 145 CA LYS A 21 18.207 11.866 14.926 1.00132.93 C ATOM 146 C LYS A 21 18.308 13.380 14.886 1.00132.93 C ATOM 147 O LYS A 21 18.192 14.076 15.892 1.00132.93 O ATOM 148 CB LYS A 21 19.188 11.373 13.854 1.00132.93 C ATOM 149 CG LYS A 21 19.637 9.926 14.023 1.00132.93 C ATOM 150 CD LYS A 21 20.282 9.348 12.766 1.00132.93 C ATOM 151 CE LYS A 21 21.401 8.357 13.076 1.00132.93 C ATOM 152 NZ LYS A 21 21.774 7.624 11.851 1.00132.93 N ATOM 153 N CYS A 22 18.424 13.910 13.642 1.00104.62 N ATOM 154 CA CYS A 22 18.703 15.280 13.262 1.00104.62 C ATOM 155 C CYS A 22 20.190 15.532 13.455 1.00104.62 C ATOM 156 O CYS A 22 20.916 15.869 12.518 1.00104.62 O ATOM 157 CB CYS A 22 17.925 16.281 14.137 1.00104.62 C ATOM 158 SG CYS A 22 18.041 18.017 13.618 1.00104.62 S ATOM 159 N TYR A 23 20.699 15.262 14.673 1.00 87.22 N ATOM 160 CA TYR A 23 22.096 15.352 15.027 1.00 87.22 C ATOM 161 C TYR A 23 22.758 16.572 14.434 1.00 87.22 C ATOM 162 O TYR A 23 23.798 16.461 13.789 1.00 87.22 O ATOM 163 CB TYR A 23 22.889 14.081 14.648 1.00 87.22 C ATOM 164 CG TYR A 23 24.230 14.150 15.301 1.00 87.22 C ATOM 165 CD1 TYR A 23 24.337 13.936 16.655 1.00 87.22 C ATOM 166 CD2 TYR A 23 25.380 14.392 14.584 1.00 87.22 C ATOM 167 CE1 TYR A 23 25.557 13.994 17.285 1.00 87.22 C ATOM 168 CE2 TYR A 23 26.604 14.452 15.207 1.00 87.22 C ATOM 169 CZ TYR A 23 26.694 14.262 16.564 1.00 87.22 C ATOM 170 OH TYR A 23 27.948 14.328 17.206 1.00 87.22 O ATOM 171 N THR A 24 22.185 17.780 14.619 1.00129.83 N ATOM 172 CA THR A 24 22.845 18.954 14.111 1.00129.83 C ATOM 173 C THR A 24 22.652 20.059 15.111 1.00129.83 C ATOM 174 O THR A 24 21.555 20.266 15.629 1.00129.83 O ATOM 175 CB THR A 24 22.330 19.367 12.756 1.00129.83 C ATOM 176 OG1 THR A 24 23.008 20.522 12.281 1.00129.83 O ATOM 177 CG2 THR A 24 20.810 19.593 12.831 1.00129.83 C ATOM 178 N VAL A 25 23.736 20.814 15.379 1.00119.31 N ATOM 179 CA VAL A 25 23.759 21.823 16.397 1.00119.31 C ATOM 180 C VAL A 25 22.853 22.965 16.060 1.00119.31 C ATOM 181 O VAL A 25 22.804 23.440 14.928 1.00119.31 O ATOM 182 CB VAL A 25 25.134 22.373 16.653 1.00119.31 C ATOM 183 CG1 VAL A 25 25.739 22.839 15.316 1.00119.31 C ATOM 184 CG2 VAL A 25 25.015 23.495 17.695 1.00119.31 C ATOM 185 N GLN A 26 22.155 23.443 17.114 1.00121.43 N ATOM 186 CA GLN A 26 21.188 24.505 17.196 1.00121.43 C ATOM 187 C GLN A 26 19.878 24.087 16.615 1.00121.43 C ATOM 188 O GLN A 26 18.904 24.828 16.729 1.00121.43 O ATOM 189 CB GLN A 26 21.624 25.827 16.521 1.00121.43 C ATOM 190 CG GLN A 26 20.627 26.982 16.712 1.00121.43 C ATOM 191 CD GLN A 26 21.197 28.248 16.083 1.00121.43 C ATOM 192 OE1 GLN A 26 21.167 29.322 16.685 1.00121.43 O ATOM 193 NE2 GLN A 26 21.719 28.122 14.833 1.00121.43 N ATOM 194 N CYS A 27 19.784 22.871 16.047 1.00 53.58 N ATOM 195 CA CYS A 27 18.513 22.421 15.560 1.00 53.58 C ATOM 196 C CYS A 27 18.077 21.342 16.504 1.00 53.58 C ATOM 197 O CYS A 27 18.904 20.639 17.084 1.00 53.58 O ATOM 198 CB CYS A 27 18.558 21.813 14.130 1.00 53.58 C ATOM 199 SG CYS A 27 19.101 23.004 12.853 1.00 53.58 S ATOM 200 N SER A 28 16.751 21.209 16.699 1.00 84.06 N ATOM 201 CA SER A 28 16.195 20.198 17.556 1.00 84.06 C ATOM 202 C SER A 28 15.270 19.409 16.688 1.00 84.06 C ATOM 203 O SER A 28 14.970 19.817 15.570 1.00 84.06 O ATOM 204 CB SER A 28 15.348 20.772 18.707 1.00 84.06 C ATOM 205 OG SER A 28 14.750 19.718 19.447 1.00 84.06 O ATOM 206 N CYS A 29 14.819 18.227 17.148 1.00 93.98 N ATOM 207 CA CYS A 29 13.930 17.487 16.302 1.00 93.98 C ATOM 208 C CYS A 29 12.525 17.843 16.656 1.00 93.98 C ATOM 209 O CYS A 29 12.201 18.048 17.825 1.00 93.98 O ATOM 210 CB CYS A 29 14.032 15.955 16.421 1.00 93.98 C ATOM 211 SG CYS A 29 15.569 15.278 15.743 1.00 93.98 S TER 212 CYS A 29 CONECT 40 158 CONECT 96 199 CONECT 121 211 CONECT 158 40 CONECT 199 96 CONECT 211 121 MASTER 55 0 0 0 0 0 0 6 211 1 6 3 END