0.033378 0.019271 0.000000 0.000000 0.038541 0.000000 0.000000 0.000000 0.025221 0.000000 0.000000 0.000000 Lisgarten, J.N. Coll, M. Portugal, J. Wright, C.W. Aymami, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 29.960 29.960 39.650 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C16 H12 N2 232.280 5-METHYL-5H-INDOLO[3,2-B]QUINOLINE CRYPTOLEPINE non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H Y 108 N C Y 109 N C Y 110 N C Y 111 N C Y 112 N C Y 113 N C Y 114 N C Y 115 N N Y 116 N C Y 117 N C Y 118 N C Y 119 N C Y 120 N C Y 121 N C Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N O N 139 N P N 140 N O N 141 N O N 142 N O N 143 N C N 144 R C N 145 N O N 146 S C N 147 N O N 148 N C N 149 R C N 150 N N N 151 N C N 152 N O N 153 N N N 154 N C N 155 N O N 156 N C N 157 N C N 158 N C N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N O N 175 N H N 176 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing Y 113 N doub Y 114 N sing N 115 N sing Y 116 N sing N 117 N sing Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing Y 122 N sing Y 123 N doub Y 124 N doub N 125 N sing Y 126 N sing Y 127 N sing Y 128 N doub Y 129 N sing Y 130 N sing Y 131 N doub N 132 N sing Y 133 N sing N 134 N sing Y 135 N doub N 136 N sing Y 137 N sing N 138 N sing Y 139 N doub Y 140 N sing Y 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N doub N 176 N sing N 177 N sing N 178 N doub N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing US Nat.Struct.Biol. NSBIEW 2024 1072-8368 9 57 60 10.1038/nsb729 11731803 The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites. 2002 10.2210/pdb1k9g/pdb pdb_00001k9g 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 120 1 IMAGE PLATE 2000-05-26 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.1 1.0 BW7A EMBL/DESY, HAMBURG 1.1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1809.217 5'-D(*CP*CP*TP*AP*GP*G)-3' 1 syn polymer 232.280 5-METHYL-5H-INDOLO[3,2-B]QUINOLINE 2 syn non-polymer 18.015 water 37 nat water no no (DC)(DC)(DT)(DA)(DG)(DG) CCTAGG A polydeoxyribonucleotide n n n n n n 1 2.72 54.76 VAPOR DIFFUSION, HANGING DROP 6.5 Magnesium acetate, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 1.602 1 19 A 1 A 6 -0.939 A_DC1:DG6_A 1 -10.972 0.186 0.119 -0.190 -9.873 1 19 A 2 A 5 -1.057 A_DC2:DG5_A 2 -1.689 0.159 0.409 -0.140 3.578 1 20 A 3 A 4 -1.593 A_DT3:DA4_A 3 -12.349 -0.050 -0.003 -0.202 -3.578 1 20 A 4 A 3 -1.593 A_DA4:DT3_A 4 -12.349 0.050 -0.003 -0.202 9.873 1 19 A 5 A 2 -1.057 A_DG5:DC2_A 5 -1.689 -0.159 0.409 -0.140 -1.602 1 19 A 6 A 1 -0.939 A_DG6:DC1_A 6 -10.972 -0.186 0.119 -0.190 6.920 24.066 A A 1 2 1.485 A A 6 5 6.943 0.619 0.113 0.397 AA_DC1DC2:DG5DG6_AA 1 -1.938 4.654 23.982 0.529 -1.592 2.872 27.500 A A 2 3 8.306 A A 5 4 2.977 3.923 -0.468 0.112 AA_DC2DT3:DA4DG5_AA 2 3.812 -8.072 26.960 -0.633 1.829 3.225 50.945 A A 3 4 -4.267 A A 4 3 3.357 -3.668 0.000 1.853 AA_DT3DA4:DT3DA4_AA 3 0.000 0.000 50.822 2.412 0.000 2.872 27.500 A A 4 5 8.306 A A 3 2 2.977 3.923 0.468 0.112 AA_DA4DG5:DC2DT3_AA 4 -3.812 8.072 26.960 -0.633 -1.829 6.920 24.066 A A 5 6 1.485 A A 2 1 6.943 0.619 -0.113 0.397 AA_DG5DG6:DC1DC2_AA 5 1.938 -4.654 23.982 0.529 1.592 chem_comp_atom chem_comp_bond database_2 diffrn_source software struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2001-11-30 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _software.classification _software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2001-10-29 REL DR1 5-METHYL-5H-INDOLO[3,2-B]QUINOLINE HOH water DR1 7 2 DR1 DR1 7 A DR1 8 2 DR1 DR1 8 A HOH 3001 3 HOH HOH 3001 A HOH 3002 3 HOH HOH 3002 A HOH 3003 3 HOH HOH 3003 A HOH 3004 3 HOH HOH 3004 A HOH 3005 3 HOH HOH 3005 A HOH 3006 3 HOH HOH 3006 A HOH 3007 3 HOH HOH 3007 A HOH 3008 3 HOH HOH 3008 A HOH 3009 3 HOH HOH 3009 A HOH 3010 3 HOH HOH 3010 A HOH 3011 3 HOH HOH 3011 A HOH 3012 3 HOH HOH 3012 A HOH 3013 3 HOH HOH 3013 A HOH 3014 3 HOH HOH 3014 A HOH 3015 3 HOH HOH 3015 A HOH 3016 3 HOH HOH 3016 A HOH 3017 3 HOH HOH 3017 A HOH 3018 3 HOH HOH 3018 A HOH 3019 3 HOH HOH 3019 A HOH 3020 3 HOH HOH 3020 A HOH 3021 3 HOH HOH 3021 A HOH 3022 3 HOH HOH 3022 A HOH 3023 3 HOH HOH 3023 A HOH 3026 3 HOH HOH 3026 A HOH 3027 3 HOH HOH 3027 A HOH 3028 3 HOH HOH 3028 A HOH 3029 3 HOH HOH 3029 A HOH 3030 3 HOH HOH 3030 A HOH 3031 3 HOH HOH 3031 A HOH 3032 3 HOH HOH 3032 A HOH 3033 3 HOH HOH 3033 A HOH 3034 3 HOH HOH 3034 A HOH 3035 3 HOH HOH 3035 A HOH 3036 3 HOH HOH 3036 A HOH 3037 3 HOH HOH 3037 A HOH 3038 3 HOH HOH 3038 A HOH 3039 3 HOH HOH 3039 A CYT 1 n 1 DC 1 A CYT 2 n 2 DC 2 A THY 3 n 3 DT 3 A ADE 4 n 4 DA 4 A GUA 5 n 5 DG 5 A GUA 6 n 6 DG 6 A 0.2090000 0.2080000 0.2270000 167 author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_675 -x+1,-y+2,z crystal symmetry operation 0.0000000000 51.8922421948 0.0000000000 1 A A O O HOH HOH 3018 3030 1.99 1 A A O O HOH HOH 3010 3012 2.03 1 A A C5' O DT HOH 3 3038 2.13 1 -4.64 0.70 108.00 103.36 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.66 0.50 119.90 123.56 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 3.12 0.50 121.00 124.12 A A A C5 C6 N1 DC DC DC 2 2 2 N 1 -5.36 0.80 102.40 97.04 A A A C3' C2' C1' DT DT DT 3 3 3 N 1 -4.23 0.60 119.00 114.77 A A A C4 C5 C7 DT DT DT 3 3 3 N 1 8.29 1.20 119.70 127.99 A A A C3' O3' P DT DT DA 3 3 4 Y 1 -4.96 0.70 108.00 103.04 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 -4.61 0.50 129.30 124.69 A A A N1 C2 N3 DA DA DA 4 4 4 N 1 10.12 1.60 120.90 131.02 A A A P O5' C5' DG DG DG 6 6 6 N 1 A A O O HOH HOH 3026 3029 2.12 1_555 3_564 0.2270000 0.2080000 0.2090000 0.2090000 1.4 10. 167 3356 3356 RANDOM 1 THROUGHOUT 0 MOLECULAR REPLACEMENT Engh & Huber 1.4 10. 37 193 36 120 0 0.011 0.023 17.7 1.4 20 1K9G 3543 3356 2 1 0.0380000 1 29.1 87.3 0.3300000 1.4 1.45 2.4 292 73.2 phasing AMoRE refinement SHELXL-97 data collection MAR345 data scaling SCALEPACK Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2 1 N N 2 N N 2 N N 3 N N The double helix is generated by the operation -x,-y+2,z. hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 4_675 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 4_675 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 4_675 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 5 A N1 DG 5 4_675 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 5 A O6 DG 5 4_675 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 5 A N2 DG 5 4_675 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 A DA 4 A N1 DA 4 4_675 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 A DA 4 A N6 DA 4 4_675 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 A DT 3 A N3 DT 3 4_675 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 A DT 3 A O4 DT 3 4_675 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 A DC 2 A N3 DC 2 4_675 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 A DC 2 A O2 DC 2 4_675 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 A DC 2 A N4 DC 2 4_675 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 4_675 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 4_675 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 4_675 DNA DNA intercalator complex, DNA 1K9G PDB 1 1K9G 1 6 1K9G 1 6 1K9G A 1 1 6 BINDING SITE FOR RESIDUE DR1 A 7 A DR1 7 Software 4 BINDING SITE FOR RESIDUE DR1 A 8 A DR1 8 Software 6 A DC 1 A DC 1 4 1_555 A DC 2 A DC 2 4 1_555 A DG 5 A DG 5 4 4_675 A DG 6 A DG 6 4 4_675 A DC 1 A DC 1 6 1_555 A DC 1 A DC 1 6 4_665 A DG 6 A DG 6 6 4_675 A DG 6 A DG 6 6 1_545 A HOH 3015 D HOH 6 4_675 A HOH 3015 D HOH 6 1_545 172 P 64