data_3WDM # _model_server_result.job_id kQNMjb2iUS_pCZAILg6GuQ _model_server_result.datetime_utc '2024-11-26 02:00:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3wdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 3WDM # _exptl.entry_id 3WDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.07 _cell.angle_gamma 90 _cell.entry_id 3WDM _cell.length_a 79.802 _cell.length_b 80.814 _cell.length_c 84.225 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H,K,L 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 3WDM _atom_sites.fract_transf_matrix[1][1] 0.012531 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004577 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012374 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01264 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 ADN A 1 901 901 ADN ADN . F 2 ADN B 1 301 902 ADN ADN . G 2 ADN C 1 301 903 ADN ADN . H 2 ADN D 1 301 904 ADN ADN . I 3 HOH A 1 1001 2 HOH TIP . I 3 HOH A 2 1002 8 HOH TIP . I 3 HOH A 3 1003 10 HOH TIP . I 3 HOH A 4 1004 15 HOH TIP . I 3 HOH A 5 1005 17 HOH TIP . I 3 HOH A 6 1006 18 HOH TIP . I 3 HOH A 7 1007 25 HOH TIP . I 3 HOH A 8 1008 30 HOH TIP . I 3 HOH A 9 1009 32 HOH TIP . I 3 HOH A 10 1010 33 HOH TIP . I 3 HOH A 11 1011 40 HOH TIP . I 3 HOH A 12 1012 48 HOH TIP . I 3 HOH A 13 1013 53 HOH TIP . I 3 HOH A 14 1014 54 HOH TIP . I 3 HOH A 15 1015 55 HOH TIP . I 3 HOH A 16 1016 58 HOH TIP . I 3 HOH A 17 1017 62 HOH TIP . I 3 HOH A 18 1018 68 HOH TIP . I 3 HOH A 19 1019 69 HOH TIP . I 3 HOH A 20 1020 70 HOH TIP . I 3 HOH A 21 1021 71 HOH TIP . I 3 HOH A 22 1022 75 HOH TIP . I 3 HOH A 23 1023 82 HOH TIP . I 3 HOH A 24 1024 83 HOH TIP . I 3 HOH A 25 1025 85 HOH TIP . I 3 HOH A 26 1026 87 HOH TIP . I 3 HOH A 27 1027 99 HOH TIP . I 3 HOH A 28 1028 100 HOH TIP . I 3 HOH A 29 1029 103 HOH TIP . I 3 HOH A 30 1030 104 HOH TIP . I 3 HOH A 31 1031 107 HOH TIP . I 3 HOH A 32 1032 108 HOH TIP . I 3 HOH A 33 1033 109 HOH TIP . I 3 HOH A 34 1034 112 HOH TIP . I 3 HOH A 35 1035 116 HOH TIP . I 3 HOH A 36 1036 118 HOH TIP . I 3 HOH A 37 1037 125 HOH TIP . I 3 HOH A 38 1038 126 HOH TIP . I 3 HOH A 39 1039 127 HOH TIP . I 3 HOH A 40 1040 129 HOH TIP . I 3 HOH A 41 1041 130 HOH TIP . I 3 HOH A 42 1042 131 HOH TIP . I 3 HOH A 43 1043 138 HOH TIP . I 3 HOH A 44 1044 141 HOH TIP . I 3 HOH A 45 1045 142 HOH TIP . I 3 HOH A 46 1046 144 HOH TIP . I 3 HOH A 47 1047 148 HOH TIP . I 3 HOH A 48 1048 149 HOH TIP . I 3 HOH A 49 1049 150 HOH TIP . I 3 HOH A 50 1050 151 HOH TIP . I 3 HOH A 51 1051 155 HOH TIP . I 3 HOH A 52 1052 158 HOH TIP . I 3 HOH A 53 1053 160 HOH TIP . I 3 HOH A 54 1054 161 HOH TIP . I 3 HOH A 55 1055 162 HOH TIP . I 3 HOH A 56 1056 163 HOH TIP . I 3 HOH A 57 1057 164 HOH TIP . I 3 HOH A 58 1058 166 HOH TIP . I 3 HOH A 59 1059 168 HOH TIP . I 3 HOH A 60 1060 170 HOH TIP . I 3 HOH A 61 1061 172 HOH TIP . I 3 HOH A 62 1062 173 HOH TIP . I 3 HOH A 63 1063 176 HOH TIP . I 3 HOH A 64 1064 183 HOH TIP . I 3 HOH A 65 1065 184 HOH TIP . I 3 HOH A 66 1066 186 HOH TIP . I 3 HOH A 67 1067 187 HOH TIP . I 3 HOH A 68 1068 188 HOH TIP . I 3 HOH A 69 1069 191 HOH TIP . I 3 HOH A 70 1070 193 HOH TIP . I 3 HOH A 71 1071 195 HOH TIP . I 3 HOH A 72 1072 196 HOH TIP . I 3 HOH A 73 1073 199 HOH TIP . I 3 HOH A 74 1074 200 HOH TIP . I 3 HOH A 75 1075 207 HOH TIP . J 3 HOH B 1 401 11 HOH TIP . J 3 HOH B 2 402 20 HOH TIP . J 3 HOH B 3 403 21 HOH TIP . J 3 HOH B 4 404 29 HOH TIP . J 3 HOH B 5 405 31 HOH TIP . J 3 HOH B 6 406 39 HOH TIP . J 3 HOH B 7 407 49 HOH TIP . J 3 HOH B 8 408 61 HOH TIP . J 3 HOH B 9 409 73 HOH TIP . J 3 HOH B 10 410 74 HOH TIP . J 3 HOH B 11 411 89 HOH TIP . J 3 HOH B 12 412 92 HOH TIP . J 3 HOH B 13 413 101 HOH TIP . J 3 HOH B 14 414 105 HOH TIP . J 3 HOH B 15 415 119 HOH TIP . J 3 HOH B 16 416 120 HOH TIP . J 3 HOH B 17 417 123 HOH TIP . J 3 HOH B 18 418 128 HOH TIP . J 3 HOH B 19 419 134 HOH TIP . J 3 HOH B 20 420 136 HOH TIP . J 3 HOH B 21 421 139 HOH TIP . J 3 HOH B 22 422 145 HOH TIP . J 3 HOH B 23 423 146 HOH TIP . J 3 HOH B 24 424 165 HOH TIP . J 3 HOH B 25 425 171 HOH TIP . J 3 HOH B 26 426 177 HOH TIP . J 3 HOH B 27 427 178 HOH TIP . J 3 HOH B 28 428 180 HOH TIP . J 3 HOH B 29 429 181 HOH TIP . J 3 HOH B 30 430 182 HOH TIP . J 3 HOH B 31 431 189 HOH TIP . J 3 HOH B 32 432 192 HOH TIP . J 3 HOH B 33 433 201 HOH TIP . J 3 HOH B 34 434 202 HOH TIP . J 3 HOH B 35 435 208 HOH TIP . J 3 HOH B 36 436 209 HOH TIP . K 3 HOH C 1 401 1 HOH TIP . K 3 HOH C 2 402 3 HOH TIP . K 3 HOH C 3 403 4 HOH TIP . K 3 HOH C 4 404 5 HOH TIP . K 3 HOH C 5 405 7 HOH TIP . K 3 HOH C 6 406 9 HOH TIP . K 3 HOH C 7 407 12 HOH TIP . K 3 HOH C 8 408 13 HOH TIP . K 3 HOH C 9 409 14 HOH TIP . K 3 HOH C 10 410 22 HOH TIP . K 3 HOH C 11 411 23 HOH TIP . K 3 HOH C 12 412 24 HOH TIP . K 3 HOH C 13 413 27 HOH TIP . K 3 HOH C 14 414 28 HOH TIP . K 3 HOH C 15 415 34 HOH TIP . K 3 HOH C 16 416 35 HOH TIP . K 3 HOH C 17 417 37 HOH TIP . K 3 HOH C 18 418 43 HOH TIP . K 3 HOH C 19 419 46 HOH TIP . K 3 HOH C 20 420 47 HOH TIP . K 3 HOH C 21 421 50 HOH TIP . K 3 HOH C 22 422 51 HOH TIP . K 3 HOH C 23 423 52 HOH TIP . K 3 HOH C 24 424 56 HOH TIP . K 3 HOH C 25 425 60 HOH TIP . K 3 HOH C 26 426 63 HOH TIP . K 3 HOH C 27 427 64 HOH TIP . K 3 HOH C 28 428 66 HOH TIP . K 3 HOH C 29 429 67 HOH TIP . K 3 HOH C 30 430 72 HOH TIP . K 3 HOH C 31 431 77 HOH TIP . K 3 HOH C 32 432 78 HOH TIP . K 3 HOH C 33 433 81 HOH TIP . K 3 HOH C 34 434 84 HOH TIP . K 3 HOH C 35 435 86 HOH TIP . K 3 HOH C 36 436 90 HOH TIP . K 3 HOH C 37 437 95 HOH TIP . K 3 HOH C 38 438 96 HOH TIP . K 3 HOH C 39 439 102 HOH TIP . K 3 HOH C 40 440 110 HOH TIP . K 3 HOH C 41 441 111 HOH TIP . K 3 HOH C 42 442 113 HOH TIP . K 3 HOH C 43 443 114 HOH TIP . K 3 HOH C 44 444 115 HOH TIP . K 3 HOH C 45 445 122 HOH TIP . K 3 HOH C 46 446 133 HOH TIP . K 3 HOH C 47 447 135 HOH TIP . K 3 HOH C 48 448 137 HOH TIP . K 3 HOH C 49 449 140 HOH TIP . K 3 HOH C 50 450 147 HOH TIP . K 3 HOH C 51 451 152 HOH TIP . K 3 HOH C 52 452 153 HOH TIP . K 3 HOH C 53 453 154 HOH TIP . K 3 HOH C 54 454 157 HOH TIP . K 3 HOH C 55 455 159 HOH TIP . K 3 HOH C 56 456 167 HOH TIP . K 3 HOH C 57 457 169 HOH TIP . K 3 HOH C 58 458 175 HOH TIP . K 3 HOH C 59 459 179 HOH TIP . K 3 HOH C 60 460 185 HOH TIP . K 3 HOH C 61 461 190 HOH TIP . K 3 HOH C 62 462 194 HOH TIP . K 3 HOH C 63 463 197 HOH TIP . K 3 HOH C 64 464 198 HOH TIP . K 3 HOH C 65 465 203 HOH TIP . K 3 HOH C 66 466 204 HOH TIP . K 3 HOH C 67 467 210 HOH TIP . L 3 HOH D 1 401 6 HOH TIP . L 3 HOH D 2 402 16 HOH TIP . L 3 HOH D 3 403 19 HOH TIP . L 3 HOH D 4 404 26 HOH TIP . L 3 HOH D 5 405 36 HOH TIP . L 3 HOH D 6 406 38 HOH TIP . L 3 HOH D 7 407 41 HOH TIP . L 3 HOH D 8 408 42 HOH TIP . L 3 HOH D 9 409 44 HOH TIP . L 3 HOH D 10 410 45 HOH TIP . L 3 HOH D 11 411 57 HOH TIP . L 3 HOH D 12 412 59 HOH TIP . L 3 HOH D 13 413 65 HOH TIP . L 3 HOH D 14 414 76 HOH TIP . L 3 HOH D 15 415 79 HOH TIP . L 3 HOH D 16 416 80 HOH TIP . L 3 HOH D 17 417 88 HOH TIP . L 3 HOH D 18 418 91 HOH TIP . L 3 HOH D 19 419 93 HOH TIP . L 3 HOH D 20 420 94 HOH TIP . L 3 HOH D 21 421 97 HOH TIP . L 3 HOH D 22 422 98 HOH TIP . L 3 HOH D 23 423 106 HOH TIP . L 3 HOH D 24 424 117 HOH TIP . L 3 HOH D 25 425 121 HOH TIP . L 3 HOH D 26 426 124 HOH TIP . L 3 HOH D 27 427 132 HOH TIP . L 3 HOH D 28 428 143 HOH TIP . L 3 HOH D 29 429 156 HOH TIP . L 3 HOH D 30 430 174 HOH TIP . L 3 HOH D 31 431 205 HOH TIP . L 3 HOH D 32 432 206 HOH TIP . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' ADN . . . F 2 -9.218 2.327 30.48 1 56.4 ? O5' ADN 301 B 1 HETATM 2 C C5' ADN . . . F 2 -8.036 1.663 30.063 1 51.05 ? C5' ADN 301 B 1 HETATM 3 C C4' ADN . . . F 2 -8.378 0.628 28.98 1 52.17 ? C4' ADN 301 B 1 HETATM 4 O O4' ADN . . . F 2 -8.932 1.252 27.787 1 50.71 ? O4' ADN 301 B 1 HETATM 5 C C3' ADN . . . F 2 -7.122 -0.102 28.51 1 50.26 ? C3' ADN 301 B 1 HETATM 6 O O3' ADN . . . F 2 -6.973 -1.324 29.215 1 52.46 ? O3' ADN 301 B 1 HETATM 7 C C2' ADN . . . F 2 -7.316 -0.322 26.999 1 50.21 ? C2' ADN 301 B 1 HETATM 8 O O2' ADN . . . F 2 -7.261 -1.714 26.675 1 54.33 ? O2' ADN 301 B 1 HETATM 9 C C1' ADN . . . F 2 -8.706 0.277 26.729 1 49.23 ? C1' ADN 301 B 1 HETATM 10 N N9 ADN . . . F 2 -8.793 0.905 25.403 1 46.63 ? N9 ADN 301 B 1 HETATM 11 C C8 ADN . . . F 2 -8.089 1.995 24.939 1 45.25 ? C8 ADN 301 B 1 HETATM 12 N N7 ADN . . . F 2 -8.443 2.271 23.713 1 43.19 ? N7 ADN 301 B 1 HETATM 13 C C5 ADN . . . F 2 -9.393 1.387 23.314 1 43.18 ? C5 ADN 301 B 1 HETATM 14 C C6 ADN . . . F 2 -10.154 1.182 22.117 1 42.1 ? C6 ADN 301 B 1 HETATM 15 N N6 ADN . . . F 2 -9.982 2.016 21.017 1 38.84 ? N6 ADN 301 B 1 HETATM 16 N N1 ADN . . . F 2 -11.046 0.158 22.087 1 39.57 ? N1 ADN 301 B 1 HETATM 17 C C2 ADN . . . F 2 -11.227 -0.658 23.136 1 40.19 ? C2 ADN 301 B 1 HETATM 18 N N3 ADN . . . F 2 -10.537 -0.503 24.271 1 42.3 ? N3 ADN 301 B 1 HETATM 19 C C4 ADN . . . F 2 -9.625 0.494 24.4 1 43.32 ? C4 ADN 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #