data_2QCH # _model_server_result.job_id 904VTJvbJ46AxPuBiVbYMA _model_server_result.datetime_utc '2024-10-14 08:20:13' _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 2qch # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":3}' # _entry.id 2QCH # _exptl.entry_id 2QCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 434.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.27 _cell.angle_gamma 90 _cell.entry_id 2QCH _cell.length_a 69.58 _cell.length_b 61.998 _cell.length_c 70.565 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 3 D N N ? 3 G N N # _chem_comp.formula 'C9 H12 I N2 O8 P' _chem_comp.formula_weight 434.078 _chem_comp.id 5IU _chem_comp.mon_nstd_flag n _chem_comp.name "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 N1 C2 5IU sing 1 n n N1 C6 5IU sing 2 n n N1 C1' 5IU sing 3 n n C2 N3 5IU sing 4 n n C2 O2 5IU doub 5 n n N3 C4 5IU sing 6 n n N3 HN3 5IU sing 7 n n C4 C5 5IU sing 8 n n C4 O4 5IU doub 9 n n C5 C6 5IU doub 10 n n C5 I5 5IU sing 11 n n C6 H6 5IU sing 12 n n C1' C2' 5IU sing 13 n n C1' O4' 5IU sing 14 n n C1' H1' 5IU sing 15 n n C2' C3' 5IU sing 16 n n C2' H2' 5IU sing 17 n n C2' "H2''" 5IU sing 18 n n C3' C4' 5IU sing 19 n n C3' O3' 5IU sing 20 n n C3' H3' 5IU sing 21 n n C4' O4' 5IU sing 22 n n C4' C5' 5IU sing 23 n n C4' H4' 5IU sing 24 n n O3' HO3' 5IU sing 25 n n C5' O5' 5IU sing 26 n n C5' H5' 5IU sing 27 n n C5' "H5''" 5IU sing 28 n n O5' P 5IU sing 29 n n P OP1 5IU doub 30 n n P OP2 5IU sing 31 n n P OP3 5IU sing 32 n n OP2 HOP2 5IU sing 33 n n OP3 HOP3 5IU sing 34 n n # _atom_sites.entry_id 2QCH _atom_sites.fract_transf_matrix[1][1] 0.014372 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00618 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01613 _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] 0.015426 _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 C 2 IOD A 1 5 5 IOD IOD . D 3 5IU A 1 1 1 5IU IU5 . E 4 UMP A 1 2 2 UMP UMP . F 2 IOD B 1 6 6 IOD IOD . G 3 5IU B 1 3 3 5IU IU5 . H 4 UMP B 1 4 4 UMP UMP . I 5 HOH A 1 481 2 HOH HOH . I 5 HOH A 2 482 5 HOH HOH . I 5 HOH A 3 483 7 HOH HOH . I 5 HOH A 4 484 8 HOH HOH . I 5 HOH A 5 485 9 HOH HOH . I 5 HOH A 6 486 12 HOH HOH . I 5 HOH A 7 487 17 HOH HOH . I 5 HOH A 8 488 25 HOH HOH . I 5 HOH A 9 489 26 HOH HOH . I 5 HOH A 10 490 27 HOH HOH . I 5 HOH A 11 491 28 HOH HOH . I 5 HOH A 12 492 30 HOH HOH . I 5 HOH A 13 493 31 HOH HOH . I 5 HOH A 14 494 36 HOH HOH . I 5 HOH A 15 495 38 HOH HOH . I 5 HOH A 16 496 41 HOH HOH . I 5 HOH A 17 497 45 HOH HOH . I 5 HOH A 18 498 47 HOH HOH . I 5 HOH A 19 499 48 HOH HOH . I 5 HOH A 20 500 49 HOH HOH . I 5 HOH A 21 501 50 HOH HOH . I 5 HOH A 22 502 51 HOH HOH . I 5 HOH A 23 503 52 HOH HOH . I 5 HOH A 24 504 53 HOH HOH . I 5 HOH A 25 505 54 HOH HOH . I 5 HOH A 26 506 55 HOH HOH . I 5 HOH A 27 507 56 HOH HOH . I 5 HOH A 28 508 57 HOH HOH . I 5 HOH A 29 509 58 HOH HOH . I 5 HOH A 30 510 61 HOH HOH . I 5 HOH A 31 511 63 HOH HOH . I 5 HOH A 32 512 64 HOH HOH . I 5 HOH A 33 513 65 HOH HOH . I 5 HOH A 34 514 66 HOH HOH . I 5 HOH A 35 515 67 HOH HOH . I 5 HOH A 36 516 68 HOH HOH . I 5 HOH A 37 517 69 HOH HOH . I 5 HOH A 38 518 70 HOH HOH . I 5 HOH A 39 519 71 HOH HOH . I 5 HOH A 40 520 72 HOH HOH . I 5 HOH A 41 521 74 HOH HOH . I 5 HOH A 42 522 76 HOH HOH . I 5 HOH A 43 523 78 HOH HOH . I 5 HOH A 44 524 84 HOH HOH . I 5 HOH A 45 525 87 HOH HOH . I 5 HOH A 46 526 88 HOH HOH . I 5 HOH A 47 527 89 HOH HOH . I 5 HOH A 48 528 90 HOH HOH . I 5 HOH A 49 529 94 HOH HOH . I 5 HOH A 50 530 99 HOH HOH . I 5 HOH A 51 531 102 HOH HOH . I 5 HOH A 52 532 103 HOH HOH . I 5 HOH A 53 533 105 HOH HOH . I 5 HOH A 54 534 107 HOH HOH . I 5 HOH A 55 535 108 HOH HOH . I 5 HOH A 56 536 112 HOH HOH . I 5 HOH A 57 537 113 HOH HOH . I 5 HOH A 58 538 114 HOH HOH . I 5 HOH A 59 539 115 HOH HOH . I 5 HOH A 60 540 120 HOH HOH . I 5 HOH A 61 541 121 HOH HOH . I 5 HOH A 62 542 122 HOH HOH . I 5 HOH A 63 543 123 HOH HOH . I 5 HOH A 64 544 125 HOH HOH . I 5 HOH A 65 545 126 HOH HOH . I 5 HOH A 66 546 128 HOH HOH . I 5 HOH A 67 547 131 HOH HOH . I 5 HOH A 68 548 132 HOH HOH . I 5 HOH A 69 549 133 HOH HOH . I 5 HOH A 70 550 134 HOH HOH . I 5 HOH A 71 551 135 HOH HOH . I 5 HOH A 72 552 137 HOH HOH . I 5 HOH A 73 553 138 HOH HOH . I 5 HOH A 74 554 145 HOH HOH . I 5 HOH A 75 555 146 HOH HOH . I 5 HOH A 76 556 148 HOH HOH . I 5 HOH A 77 557 150 HOH HOH . I 5 HOH A 78 558 151 HOH HOH . I 5 HOH A 79 559 156 HOH HOH . I 5 HOH A 80 560 162 HOH HOH . I 5 HOH A 81 561 163 HOH HOH . I 5 HOH A 82 562 165 HOH HOH . I 5 HOH A 83 563 168 HOH HOH . I 5 HOH A 84 564 170 HOH HOH . I 5 HOH A 85 565 171 HOH HOH . I 5 HOH A 86 566 174 HOH HOH . I 5 HOH A 87 567 181 HOH HOH . I 5 HOH A 88 568 183 HOH HOH . I 5 HOH A 89 569 184 HOH HOH . I 5 HOH A 90 570 185 HOH HOH . I 5 HOH A 91 571 188 HOH HOH . I 5 HOH A 92 572 189 HOH HOH . I 5 HOH A 93 573 191 HOH HOH . I 5 HOH A 94 574 192 HOH HOH . I 5 HOH A 95 575 193 HOH HOH . I 5 HOH A 96 576 194 HOH HOH . I 5 HOH A 97 577 197 HOH HOH . I 5 HOH A 98 578 199 HOH HOH . I 5 HOH A 99 579 201 HOH HOH . I 5 HOH A 100 580 202 HOH HOH . I 5 HOH A 101 581 204 HOH HOH . I 5 HOH A 102 582 205 HOH HOH . I 5 HOH A 103 583 206 HOH HOH . I 5 HOH A 104 584 214 HOH HOH . I 5 HOH A 105 585 215 HOH HOH . I 5 HOH A 106 586 219 HOH HOH . I 5 HOH A 107 587 222 HOH HOH . I 5 HOH A 108 588 224 HOH HOH . I 5 HOH A 109 589 225 HOH HOH . I 5 HOH A 110 590 226 HOH HOH . I 5 HOH A 111 591 234 HOH HOH . I 5 HOH A 112 592 235 HOH HOH . J 5 HOH B 1 481 1 HOH HOH . J 5 HOH B 2 482 3 HOH HOH . J 5 HOH B 3 483 4 HOH HOH . J 5 HOH B 4 484 6 HOH HOH . J 5 HOH B 5 485 10 HOH HOH . J 5 HOH B 6 486 11 HOH HOH . J 5 HOH B 7 487 13 HOH HOH . J 5 HOH B 8 488 14 HOH HOH . J 5 HOH B 9 489 15 HOH HOH . J 5 HOH B 10 490 16 HOH HOH . J 5 HOH B 11 491 18 HOH HOH . J 5 HOH B 12 492 19 HOH HOH . J 5 HOH B 13 493 20 HOH HOH . J 5 HOH B 14 494 21 HOH HOH . J 5 HOH B 15 495 22 HOH HOH . J 5 HOH B 16 496 23 HOH HOH . J 5 HOH B 17 497 24 HOH HOH . J 5 HOH B 18 498 29 HOH HOH . J 5 HOH B 19 499 32 HOH HOH . J 5 HOH B 20 500 33 HOH HOH . J 5 HOH B 21 501 34 HOH HOH . J 5 HOH B 22 502 35 HOH HOH . J 5 HOH B 23 503 37 HOH HOH . J 5 HOH B 24 504 39 HOH HOH . J 5 HOH B 25 505 40 HOH HOH . J 5 HOH B 26 506 42 HOH HOH . J 5 HOH B 27 507 43 HOH HOH . J 5 HOH B 28 508 44 HOH HOH . J 5 HOH B 29 509 46 HOH HOH . J 5 HOH B 30 510 59 HOH HOH . J 5 HOH B 31 511 60 HOH HOH . J 5 HOH B 32 512 62 HOH HOH . J 5 HOH B 33 513 73 HOH HOH . J 5 HOH B 34 514 77 HOH HOH . J 5 HOH B 35 515 79 HOH HOH . J 5 HOH B 36 516 80 HOH HOH . J 5 HOH B 37 517 81 HOH HOH . J 5 HOH B 38 518 82 HOH HOH . J 5 HOH B 39 519 83 HOH HOH . J 5 HOH B 40 520 85 HOH HOH . J 5 HOH B 41 521 91 HOH HOH . J 5 HOH B 42 522 92 HOH HOH . J 5 HOH B 43 523 95 HOH HOH . J 5 HOH B 44 524 96 HOH HOH . J 5 HOH B 45 525 97 HOH HOH . J 5 HOH B 46 526 98 HOH HOH . J 5 HOH B 47 527 100 HOH HOH . J 5 HOH B 48 528 101 HOH HOH . J 5 HOH B 49 529 104 HOH HOH . J 5 HOH B 50 530 106 HOH HOH . J 5 HOH B 51 531 109 HOH HOH . J 5 HOH B 52 532 110 HOH HOH . J 5 HOH B 53 533 111 HOH HOH . J 5 HOH B 54 534 116 HOH HOH . J 5 HOH B 55 535 117 HOH HOH . J 5 HOH B 56 536 118 HOH HOH . J 5 HOH B 57 537 119 HOH HOH . J 5 HOH B 58 538 127 HOH HOH . J 5 HOH B 59 539 129 HOH HOH . J 5 HOH B 60 540 130 HOH HOH . J 5 HOH B 61 541 136 HOH HOH . J 5 HOH B 62 542 139 HOH HOH . J 5 HOH B 63 543 140 HOH HOH . J 5 HOH B 64 544 141 HOH HOH . J 5 HOH B 65 545 142 HOH HOH . J 5 HOH B 66 546 143 HOH HOH . J 5 HOH B 67 547 144 HOH HOH . J 5 HOH B 68 548 147 HOH HOH . J 5 HOH B 69 549 149 HOH HOH . J 5 HOH B 70 550 152 HOH HOH . J 5 HOH B 71 551 154 HOH HOH . J 5 HOH B 72 552 155 HOH HOH . J 5 HOH B 73 553 157 HOH HOH . J 5 HOH B 74 554 158 HOH HOH . J 5 HOH B 75 555 159 HOH HOH . J 5 HOH B 76 556 160 HOH HOH . J 5 HOH B 77 557 161 HOH HOH . J 5 HOH B 78 558 166 HOH HOH . J 5 HOH B 79 559 167 HOH HOH . J 5 HOH B 80 560 169 HOH HOH . J 5 HOH B 81 561 172 HOH HOH . J 5 HOH B 82 562 173 HOH HOH . J 5 HOH B 83 563 175 HOH HOH . J 5 HOH B 84 564 176 HOH HOH . J 5 HOH B 85 565 177 HOH HOH . J 5 HOH B 86 566 178 HOH HOH . J 5 HOH B 87 567 179 HOH HOH . J 5 HOH B 88 568 180 HOH HOH . J 5 HOH B 89 569 182 HOH HOH . J 5 HOH B 90 570 186 HOH HOH . J 5 HOH B 91 571 187 HOH HOH . J 5 HOH B 92 572 190 HOH HOH . J 5 HOH B 93 573 195 HOH HOH . J 5 HOH B 94 574 196 HOH HOH . J 5 HOH B 95 575 198 HOH HOH . J 5 HOH B 96 576 200 HOH HOH . J 5 HOH B 97 577 203 HOH HOH . J 5 HOH B 98 578 207 HOH HOH . J 5 HOH B 99 579 208 HOH HOH . J 5 HOH B 100 580 209 HOH HOH . J 5 HOH B 101 581 210 HOH HOH . J 5 HOH B 102 582 211 HOH HOH . J 5 HOH B 103 583 212 HOH HOH . J 5 HOH B 104 584 216 HOH HOH . J 5 HOH B 105 585 217 HOH HOH . J 5 HOH B 106 586 218 HOH HOH . J 5 HOH B 107 587 227 HOH HOH . J 5 HOH B 108 588 228 HOH HOH . J 5 HOH B 109 589 229 HOH HOH . J 5 HOH B 110 590 231 HOH HOH . J 5 HOH B 111 591 232 HOH HOH . J 5 HOH B 112 592 233 HOH HOH . J 5 HOH B 113 593 236 HOH HOH . J 5 HOH B 114 594 237 HOH HOH . J 5 HOH B 115 595 238 HOH HOH . J 5 HOH B 116 596 239 HOH HOH . J 5 HOH B 117 597 240 HOH HOH . # 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 N N1 5IU . . . G 3 4.924 7.667 25.872 0.3 23.85 ? N1 5IU 3 B 1 HETATM 2 C C2 5IU . . . G 3 4.05 8.564 25.214 0.3 24.05 ? C2 5IU 3 B 1 HETATM 3 N N3 5IU . . . G 3 3.587 8.301 23.977 0.3 23.89 ? N3 5IU 3 B 1 HETATM 4 C C4 5IU . . . G 3 3.924 7.184 23.322 0.3 23.8 ? C4 5IU 3 B 1 HETATM 5 C C5 5IU . . . G 3 4.828 6.228 23.995 0.3 23.83 ? C5 5IU 3 B 1 HETATM 6 C C6 5IU . . . G 3 5.287 6.534 25.269 0.3 23.91 ? C6 5IU 3 B 1 HETATM 7 O O2 5IU . . . G 3 3.702 9.624 25.775 0.3 24.06 ? O2 5IU 3 B 1 HETATM 8 O O4 5IU . . . G 3 3.481 6.951 22.172 0.3 23.82 ? O4 5IU 3 B 1 HETATM 9 I I5 5IU . . . G 3 5.432 4.445 23.074 0.3 23.8 ? I5 5IU 3 B 1 HETATM 10 C C1' 5IU . . . G 3 5.442 7.916 27.228 0.3 24.45 ? C1' 5IU 3 B 1 HETATM 11 C C2' 5IU . . . G 3 6.403 9.094 27.285 0.3 24.83 ? C2' 5IU 3 B 1 HETATM 12 C C3' 5IU . . . G 3 6.129 9.715 28.638 0.3 25.2 ? C3' 5IU 3 B 1 HETATM 13 C C4' 5IU . . . G 3 4.707 9.297 28.987 0.3 25.51 ? C4' 5IU 3 B 1 HETATM 14 O O3' 5IU . . . G 3 7.06 9.208 29.597 0.3 24.72 ? O3' 5IU 3 B 1 HETATM 15 O O4' 5IU . . . G 3 4.378 8.189 28.152 0.3 24.78 ? O4' 5IU 3 B 1 HETATM 16 C C5' 5IU . . . G 3 3.692 10.41 28.748 0.3 25.92 ? C5' 5IU 3 B 1 HETATM 17 O O5' 5IU . . . G 3 3.462 11.093 29.975 0.3 26.53 ? O5' 5IU 3 B 1 HETATM 18 P P 5IU . . . G 3 2.808 12.564 30.062 0.3 26.96 ? P 5IU 3 B 1 HETATM 19 O OP1 5IU . . . G 3 3.698 13.23 31.083 0.3 26.58 ? OP1 5IU 3 B 1 HETATM 20 O OP2 5IU . . . G 3 1.403 12.276 30.535 0.3 26.41 ? OP2 5IU 3 B 1 HETATM 21 O OP3 5IU . . . G 3 2.878 13.16 28.67 0.3 26.99 ? OP3 5IU 3 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 518 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #