data_2QCH # _model_server_result.job_id NrUb4bzavAXINx2L_vWEMA _model_server_result.datetime_utc '2024-10-14 08:25:11' _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":"E","auth_seq_id":2}' # _entry.id 2QCH # _exptl.entry_id 2QCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 ? 4 E N N ? 4 H N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 392 n n N1 C6 UMP sing 393 n n N1 C1' UMP sing 394 n n C2 N3 UMP sing 395 n n C2 O2 UMP doub 396 n n N3 C4 UMP sing 397 n n N3 HN3 UMP sing 398 n n C4 C5 UMP sing 399 n n C4 O4 UMP doub 400 n n C5 C6 UMP doub 401 n n C5 H5 UMP sing 402 n n C6 H6 UMP sing 403 n n C1' C2' UMP sing 404 n n C1' O4' UMP sing 405 n n C1' H1' UMP sing 406 n n C2' C3' UMP sing 407 n n C2' H2' UMP sing 408 n n C2' "H2''" UMP sing 409 n n C3' C4' UMP sing 410 n n C3' O3' UMP sing 411 n n C3' H3' UMP sing 412 n n C4' O4' UMP sing 413 n n C4' C5' UMP sing 414 n n C4' H4' UMP sing 415 n n O3' HO3' UMP sing 416 n n C5' O5' UMP sing 417 n n C5' H5' UMP sing 418 n n C5' "H5''" UMP sing 419 n n O5' P UMP sing 420 n n P OP1 UMP doub 421 n n P OP2 UMP sing 422 n n P OP3 UMP sing 423 n n OP2 HOP2 UMP sing 424 n n OP3 HOP3 UMP sing 425 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 UMP . . . E 4 21.135 -3.898 14.159 0.7 26.13 ? N1 UMP 2 A 1 HETATM 2 C C2 UMP . . . E 4 20.853 -4.836 13.179 0.7 25.44 ? C2 UMP 2 A 1 HETATM 3 N N3 UMP . . . E 4 19.927 -4.556 12.193 0.7 25.27 ? N3 UMP 2 A 1 HETATM 4 C C4 UMP . . . E 4 19.311 -3.321 12.174 0.7 25.41 ? C4 UMP 2 A 1 HETATM 5 C C5 UMP . . . E 4 19.605 -2.38 13.151 0.7 25.23 ? C5 UMP 2 A 1 HETATM 6 C C6 UMP . . . E 4 20.52 -2.681 14.129 0.7 25.57 ? C6 UMP 2 A 1 HETATM 7 O O2 UMP . . . E 4 21.39 -5.94 13.17 0.7 26.54 ? O2 UMP 2 A 1 HETATM 8 O O4 UMP . . . E 4 18.488 -3.048 11.307 0.7 25.2 ? O4 UMP 2 A 1 HETATM 9 C C1' UMP . . . E 4 22.133 -4.097 15.229 0.7 26.29 ? C1' UMP 2 A 1 HETATM 10 C C2' UMP . . . E 4 21.883 -5.228 16.207 0.7 26.66 ? C2' UMP 2 A 1 HETATM 11 C C3' UMP . . . E 4 23.292 -5.637 16.561 0.7 26.99 ? C3' UMP 2 A 1 HETATM 12 C C4' UMP . . . E 4 24.11 -5.339 15.31 0.7 27.33 ? C4' UMP 2 A 1 HETATM 13 O O3' UMP . . . E 4 23.742 -4.853 17.639 0.7 26.35 ? O3' UMP 2 A 1 HETATM 14 O O4' UMP . . . E 4 23.378 -4.361 14.613 0.7 27.51 ? O4' UMP 2 A 1 HETATM 15 C C5' UMP . . . E 4 24.302 -6.515 14.353 0.7 26.76 ? C5' UMP 2 A 1 HETATM 16 O O5' UMP . . . E 4 24.813 -7.635 15.032 0.7 27.36 ? O5' UMP 2 A 1 HETATM 17 P P UMP . . . E 4 25.375 -8.932 14.261 0.7 27.57 ? P UMP 2 A 1 HETATM 18 O OP1 UMP . . . E 4 25.982 -9.756 15.367 0.7 22.95 ? OP1 UMP 2 A 1 HETATM 19 O OP2 UMP . . . E 4 26.4 -8.539 13.228 0.7 26.02 ? OP2 UMP 2 A 1 HETATM 20 O OP3 UMP . . . E 4 24.3 -9.665 13.563 0.7 25.64 ? OP3 UMP 2 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 396 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #