1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 da Silva, M.W. Bierbryer, R.G. Wilds, C.J. Noronha, A.M. Colvin, O.M. Miller, P.S. Gamcsik, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C12 H19 N2 O8 P 350.262 n N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE DNA linking 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 N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N P N 145 N O N 146 N O N 147 N O N 148 N C N 149 R C N 150 N O N 151 R C N 152 N N N 153 N C N 154 N C N 155 N O N 156 N N N 157 N C N 158 N C N 159 N C N 160 N O N 161 N C N 162 N C N 163 N C N 164 S C N 165 N O N 166 N O 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 H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 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 N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub 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 doub N 169 N sing N 170 N doub N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing UK Bioorg.Med.Chem. BMECEP 1200 0968-0896 13 4580 4587 10.1016/j.bmc.2005.03.032 15953553 Intrastrand base-stacking buttresses widening of major groove in interstrand cross-linked B-DNA. 2005 10.2210/pdb1xci/pdb pdb_00001xci 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3376.263 5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3' 2 syn polymer no yes (DC)(DG)(DA)(DA)(DA)(TTM)(DT)(DT)(DT)(DC)(DG) CGAAATTTTCG A,B polydeoxyribonucleotide n n n n n n n n n n n -0.250 1 19 A 1 B 11 -1.073 A_DC1:DG11_B 1 -0.506 0.388 0.008 -0.201 -0.282 1 19 A 2 B 10 -0.318 A_DG2:DC10_B 2 -0.848 -0.247 -0.032 -0.203 0.161 1 20 A 3 B 9 -1.797 A_DA3:DT9_B 3 0.748 -0.255 0.040 -0.213 0.014 1 20 A 4 B 8 -5.386 A_DA4:DT8_B 4 -0.259 0.417 -0.015 -0.082 1.128 1 20 A 5 B 7 -5.851 A_DA5:DT7_B 5 0.345 -0.248 0.058 -0.195 -1.570 1 20 A 7 B 5 -5.527 A_DT7:DA5_B 6 2.514 0.244 -0.034 -0.199 -0.879 1 20 A 8 B 4 -4.647 A_DT8:DA4_B 7 0.928 -0.363 0.016 -0.092 -0.100 1 20 A 9 B 3 -4.006 A_DT9:DA3_B 8 0.705 0.253 0.039 -0.211 0.128 1 19 A 10 B 2 -1.429 A_DC10:DG2_B 9 -0.683 0.239 -0.023 -0.204 0.488 1 19 A 11 B 1 -0.204 A_DG11:DC1_B 10 -0.583 -0.541 0.019 -0.233 2.917 44.235 A A 1 2 -2.831 B B 11 10 2.966 -2.131 0.310 1.229 AA_DC1DG2:DC10DG11_BB 1 1.910 -2.538 44.147 1.811 -0.251 3.143 50.722 A A 2 3 -19.004 B B 10 9 3.344 -16.035 0.210 0.170 AA_DG2DA3:DT9DC10_BB 2 0.222 -0.263 48.280 1.350 -0.229 3.241 34.950 A A 3 4 6.802 B B 9 8 3.290 4.074 0.116 -0.120 AA_DA3DA4:DT8DT9_BB 3 -2.303 3.846 34.645 -0.817 -0.543 3.153 34.070 A A 4 5 -3.106 B B 8 7 3.126 -1.818 0.127 -0.852 AA_DA4DA5:DT7DT8_BB 4 -2.113 3.610 33.960 -1.176 -0.539 3.643 38.418 A A 7 8 -21.379 B B 5 4 3.420 -13.777 0.124 -1.256 AA_DT7DT8:DA4DA5_BB 5 0.074 -0.115 35.950 0.012 -0.179 3.214 32.940 A A 8 9 9.035 B B 4 3 3.397 5.093 -0.467 -0.459 AA_DT8DT9:DA3DA4_BB 6 3.831 -6.797 32.334 -1.694 1.490 3.286 49.785 A A 9 10 -20.704 B B 3 2 3.395 -17.116 0.393 -0.241 AA_DT9DC10:DG2DA3_BB 7 -0.490 0.592 46.925 1.037 -0.505 2.866 44.341 A A 10 11 -5.033 B B 2 1 2.977 -3.793 -0.406 1.432 AA_DC10DG11:DC1DG2_BB 8 -2.198 2.916 44.134 2.212 0.355 ndb_struct_conf_na pdbx_entity_src_syn pdbx_nmr_exptl_sample_conditions pdbx_struct_assembly pdbx_struct_assembly_prop pdbx_struct_oper_list chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Derived calculations Experimental preparation Source and taxonomy Data collection Database references Derived calculations 1 0 2005-08-16 1 1 2008-04-30 1 2 2011-07-13 1 3 2018-06-06 1 4 2024-05-01 _pdbx_nmr_exptl_sample_conditions.temperature _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id RCSB Y RCSB 2004-09-02 REL 32630 synthetic construct sample Structure determined using standard NMR techniques structures with the lowest energy 15 1 DQF-COSY 2D TOCSY 2D NOESY JR-NOESY 31P,1H HETCOR 100 mM NaCl 7.4 normal 293 K 100 mM NaCl 7.4 normal 273 K distance geometry, simulated annealing, molecular dynamics 1 lowest energy 1.5 mM sample in 100 mM NaCl, 50 mM phosphate pH 7.4, D2O D2O 1.5 mM sample in 100 mM NaCl, 50 mM phosphate pH 7.4, H2O H2O Brunger refinement X-PLOR 2.1 800 Varian INOVA CYT 1 n 1 DC 1 A GUA 2 n 2 DG 2 A ADE 3 n 3 DA 3 A ADE 4 n 4 DA 4 A ADE 5 n 5 DA 5 A THZ 6 n 6 TTM 6 A THY 7 n 7 DT 7 A THY 8 n 8 DT 8 A THY 9 n 9 DT 9 A CYT 10 n 10 DC 10 A GUA 11 n 11 DG 11 A CYT 1 n 1 DC 1 B GUA 2 n 2 DG 2 B ADE 3 n 3 DA 3 B ADE 4 n 4 DA 4 B ADE 5 n 5 DA 5 B THZ 6 n 6 TTM 6 B THY 7 n 7 DT 7 B THY 8 n 8 DT 8 B THY 9 n 9 DT 9 B CYT 10 n 10 DC 10 B GUA 11 n 11 DG 11 B author_defined_assembly 2 dimeric 2500 -2 3590 A TTM 6 N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE A TTM 6 DT B TTM 6 N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE B TTM 6 DT 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 -4.63 0.70 102.20 97.57 A A A C4' C3' C2' DC DC DC 1 1 1 N 1 -5.89 0.80 102.40 96.51 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 -6.17 0.80 102.40 96.23 A A A C3' C2' C1' DA DA DA 3 3 3 N 1 3.85 0.60 118.60 122.45 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 8.11 1.20 119.70 127.81 A A A C3' O3' P DA DA DA 3 3 4 Y 1 -4.48 0.70 102.20 97.72 A A A C4' C3' C2' DA DA DA 4 4 4 N 1 -7.95 0.80 102.40 94.45 A A A C3' C2' C1' DA DA DA 4 4 4 N 1 -6.53 0.80 105.90 99.37 A A A O4' C1' C2' DA DA DA 4 4 4 N 1 6.68 0.30 108.30 114.98 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 -6.06 0.80 102.40 96.34 A A A C3' C2' C1' DA DA DA 5 5 5 N 1 4.95 0.60 118.60 123.55 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 3.69 0.60 118.00 121.69 A A A C4 C5 C6 DT DT DT 7 7 7 N 1 -3.82 0.60 122.90 119.08 A A A C6 C5 C7 DT DT DT 7 7 7 N 1 -5.47 0.80 102.40 96.93 A A A C3' C2' C1' DT DT DT 8 8 8 N 1 3.96 0.60 118.00 121.96 A A A C4 C5 C6 DT DT DT 8 8 8 N 1 -5.80 0.60 122.90 117.10 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 -2.54 0.40 104.50 101.96 A A A O4' C4' C3' DT DT DT 9 9 9 N 1 -10.31 0.80 102.40 92.09 A A A C3' C2' C1' DT DT DT 9 9 9 N 1 -5.05 0.80 105.90 100.85 A A A O4' C1' C2' DT DT DT 9 9 9 N 1 3.71 0.30 108.30 112.01 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 3.74 0.60 118.00 121.74 A A A C4 C5 C6 DT DT DT 9 9 9 N 1 -4.16 0.60 122.90 118.74 A A A C6 C5 C7 DT DT DT 9 9 9 N 1 -6.16 0.80 102.40 96.24 A A A C3' C2' C1' DC DC DC 10 10 10 N 1 -3.59 0.40 104.50 100.91 A A A O4' C4' C3' DG DG DG 11 11 11 N 1 -8.41 0.80 102.40 93.99 A A A C3' C2' C1' DG DG DG 11 11 11 N 1 -6.64 0.80 102.40 95.76 B B B C3' C2' C1' DC DC DC 1 1 1 N 1 -5.78 0.80 105.90 100.12 B B B O4' C1' C2' DC DC DC 1 1 1 N 1 -3.07 0.40 104.50 101.43 B B B O4' C4' C3' DG DG DG 2 2 2 N 1 -10.56 0.80 102.40 91.84 B B B C3' C2' C1' DG DG DG 2 2 2 N 1 -6.52 0.80 102.40 95.88 B B B C3' C2' C1' DA DA DA 3 3 3 N 1 4.39 0.60 118.60 122.99 B B B N1 C6 N6 DA DA DA 3 3 3 N 1 7.54 1.20 119.70 127.24 B B B C3' O3' P DA DA DA 3 3 4 Y 1 -9.10 0.80 102.40 93.30 B B B C3' C2' C1' DA DA DA 4 4 4 N 1 3.64 0.30 108.30 111.94 B B B O4' C1' N9 DA DA DA 4 4 4 N 1 -7.19 0.80 102.40 95.21 B B B C3' C2' C1' DA DA DA 5 5 5 N 1 2.12 0.30 108.30 110.42 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 4.70 0.60 118.60 123.30 B B B N1 C6 N6 DA DA DA 5 5 5 N 1 -5.47 0.80 102.40 96.93 B B B C3' C2' C1' DT DT DT 7 7 7 N 1 -5.75 0.80 102.40 96.65 B B B C3' C2' C1' DT DT DT 8 8 8 N 1 -5.06 0.80 105.90 100.84 B B B O4' C1' C2' DT DT DT 8 8 8 N 1 1.90 0.30 108.30 110.20 B B B O4' C1' N1 DT DT DT 8 8 8 N 1 -9.45 0.80 102.40 92.95 B B B C3' C2' C1' DT DT DT 9 9 9 N 1 4.88 0.30 108.30 113.18 B B B O4' C1' N1 DT DT DT 9 9 9 N 1 -6.93 0.80 102.40 95.47 B B B C3' C2' C1' DC DC DC 10 10 10 N 1 -3.75 0.40 104.50 100.75 B B B O4' C4' C3' DG DG DG 11 11 11 N 1 -8.96 0.80 102.40 93.44 B B B C3' C2' C1' DG DG DG 11 11 11 N Mispair Aligned N3T-Butyl-N3T Interstrand Crosslink 1 N N 1 N N covale 1.600 both A DA 5 A O3' DA 5 1_555 A TTM 6 A P TTM 6 1_555 covale 1.603 both A TTM 6 A O3' TTM 6 1_555 A DT 7 A P DT 7 1_555 covale 1.621 none A TTM 6 A C2Q TTM 6 1_555 B TTM 6 B C2Q TTM 6 1_555 covale 1.603 both B DA 5 B O3' DA 5 1_555 B TTM 6 B P TTM 6 1_555 covale 1.602 both B TTM 6 B O3' TTM 6 1_555 B DT 7 B P DT 7 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 9 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 7 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 4 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 4 B N6 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 1 B N4 DC 1 1_555 DNA interstrand cross-link, double helix, DNA 1XCI PDB 1 1XCI 1 11 1XCI 1 11 1XCI A 1 1 11 1 11 1XCI 1 11 1XCI B 1 1 11