data_4Q1E # _model_server_result.job_id L89tyPJZcPXzFfk2QOcWgg _model_server_result.datetime_utc '2024-11-22 14:49:22' _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 4q1e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":303}' # _entry.id 4Q1E # _exptl.entry_id 4Q1E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 4Q1E _cell.length_a 68.736 _cell.length_b 68.736 _cell.length_c 122.206 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q1E _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _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 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 UDP sing 464 n n N1 C6 UDP sing 465 n n N1 C1' UDP sing 466 n n C2 N3 UDP sing 467 n n C2 O2 UDP doub 468 n n N3 C4 UDP sing 469 n n N3 HN3 UDP sing 470 n n C4 C5 UDP sing 471 n n C4 O4 UDP doub 472 n n C5 C6 UDP doub 473 n n C5 H5 UDP sing 474 n n C6 H6 UDP sing 475 n n C1' C2' UDP sing 476 n n C1' O4' UDP sing 477 n n C1' H1' UDP sing 478 n n C2' O2' UDP sing 479 n n C2' C3' UDP sing 480 n n C2' H2' UDP sing 481 n n O2' HO2' UDP sing 482 n n C3' C4' UDP sing 483 n n C3' O3' UDP sing 484 n n C3' H3' UDP sing 485 n n C4' O4' UDP sing 486 n n C4' C5' UDP sing 487 n n C4' H4' UDP sing 488 n n O3' HO3' UDP sing 489 n n C5' O5' UDP sing 490 n n C5' "H5'1" UDP sing 491 n n C5' "H5'2" UDP sing 492 n n O5' PA UDP sing 493 n n PA O1A UDP doub 494 n n PA O2A UDP sing 495 n n PA O3A UDP sing 496 n n O2A HOA2 UDP sing 497 n n O3A PB UDP sing 498 n n PB O1B UDP doub 499 n n PB O2B UDP sing 500 n n PB O3B UDP sing 501 n n O2B HOB2 UDP sing 502 n n O3B HOB3 UDP sing 503 n n # _atom_sites.entry_id 4Q1E _atom_sites.fract_transf_matrix[1][1] 0.014548 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014548 _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] 0.008183 _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 2Y8 A 1 301 301 2Y8 DRR . D 3 2Y7 A 1 302 302 2Y7 DRS . E 4 UDP A 1 303 401 UDP UDP . F 2 2Y8 B 1 301 301 2Y8 DRR . G 3 2Y7 B 1 302 302 2Y7 DRS . H 4 UDP B 1 303 401 UDP UDP . I 5 HOH A 1 401 1 HOH HOH . I 5 HOH A 2 402 2 HOH HOH . I 5 HOH A 3 403 3 HOH HOH . I 5 HOH A 4 404 4 HOH HOH . I 5 HOH A 5 405 5 HOH HOH . I 5 HOH A 6 406 6 HOH HOH . I 5 HOH A 7 407 7 HOH HOH . I 5 HOH A 8 408 8 HOH HOH . I 5 HOH A 9 409 9 HOH HOH . I 5 HOH A 10 410 10 HOH HOH . I 5 HOH A 11 411 11 HOH HOH . I 5 HOH A 12 412 12 HOH HOH . I 5 HOH A 13 413 13 HOH HOH . I 5 HOH A 14 414 14 HOH HOH . I 5 HOH A 15 415 15 HOH HOH . I 5 HOH A 16 416 16 HOH HOH . I 5 HOH A 17 417 17 HOH HOH . I 5 HOH A 18 418 18 HOH HOH . I 5 HOH A 19 419 19 HOH HOH . I 5 HOH A 20 420 20 HOH HOH . I 5 HOH A 21 421 21 HOH HOH . I 5 HOH A 22 422 22 HOH HOH . I 5 HOH A 23 423 23 HOH HOH . I 5 HOH A 24 424 24 HOH HOH . I 5 HOH A 25 425 25 HOH HOH . I 5 HOH A 26 426 26 HOH HOH . I 5 HOH A 27 427 27 HOH HOH . I 5 HOH A 28 428 28 HOH HOH . I 5 HOH A 29 429 29 HOH HOH . I 5 HOH A 30 430 30 HOH HOH . I 5 HOH A 31 431 31 HOH HOH . I 5 HOH A 32 432 32 HOH HOH . I 5 HOH A 33 433 33 HOH HOH . I 5 HOH A 34 434 35 HOH HOH . I 5 HOH A 35 435 36 HOH HOH . I 5 HOH A 36 436 37 HOH HOH . I 5 HOH A 37 437 38 HOH HOH . I 5 HOH A 38 438 39 HOH HOH . I 5 HOH A 39 439 40 HOH HOH . I 5 HOH A 40 440 41 HOH HOH . I 5 HOH A 41 441 42 HOH HOH . I 5 HOH A 42 442 43 HOH HOH . I 5 HOH A 43 443 44 HOH HOH . I 5 HOH A 44 444 45 HOH HOH . I 5 HOH A 45 445 46 HOH HOH . I 5 HOH A 46 446 47 HOH HOH . I 5 HOH A 47 447 48 HOH HOH . I 5 HOH A 48 448 49 HOH HOH . I 5 HOH A 49 449 50 HOH HOH . I 5 HOH A 50 450 51 HOH HOH . I 5 HOH A 51 451 52 HOH HOH . I 5 HOH A 52 452 53 HOH HOH . I 5 HOH A 53 453 54 HOH HOH . I 5 HOH A 54 454 55 HOH HOH . I 5 HOH A 55 455 56 HOH HOH . I 5 HOH A 56 456 57 HOH HOH . I 5 HOH A 57 457 58 HOH HOH . I 5 HOH A 58 458 59 HOH HOH . I 5 HOH A 59 459 60 HOH HOH . I 5 HOH A 60 460 61 HOH HOH . I 5 HOH A 61 461 62 HOH HOH . I 5 HOH A 62 462 63 HOH HOH . I 5 HOH A 63 463 64 HOH HOH . I 5 HOH A 64 464 65 HOH HOH . I 5 HOH A 65 465 66 HOH HOH . I 5 HOH A 66 466 67 HOH HOH . I 5 HOH A 67 467 68 HOH HOH . I 5 HOH A 68 468 69 HOH HOH . I 5 HOH A 69 469 70 HOH HOH . I 5 HOH A 70 470 71 HOH HOH . I 5 HOH A 71 471 72 HOH HOH . I 5 HOH A 72 472 73 HOH HOH . I 5 HOH A 73 473 74 HOH HOH . I 5 HOH A 74 474 75 HOH HOH . I 5 HOH A 75 475 76 HOH HOH . I 5 HOH A 76 476 77 HOH HOH . I 5 HOH A 77 477 78 HOH HOH . I 5 HOH A 78 478 79 HOH HOH . I 5 HOH A 79 479 80 HOH HOH . I 5 HOH A 80 480 81 HOH HOH . I 5 HOH A 81 481 82 HOH HOH . I 5 HOH A 82 482 83 HOH HOH . I 5 HOH A 83 483 84 HOH HOH . I 5 HOH A 84 484 85 HOH HOH . I 5 HOH A 85 485 86 HOH HOH . I 5 HOH A 86 486 87 HOH HOH . I 5 HOH A 87 487 88 HOH HOH . I 5 HOH A 88 488 89 HOH HOH . I 5 HOH A 89 489 91 HOH HOH . I 5 HOH A 90 490 181 HOH HOH . I 5 HOH A 91 491 182 HOH HOH . J 5 HOH B 1 401 34 HOH HOH . J 5 HOH B 2 402 90 HOH HOH . J 5 HOH B 3 403 92 HOH HOH . J 5 HOH B 4 404 93 HOH HOH . J 5 HOH B 5 405 94 HOH HOH . J 5 HOH B 6 406 95 HOH HOH . J 5 HOH B 7 407 96 HOH HOH . J 5 HOH B 8 408 97 HOH HOH . J 5 HOH B 9 409 98 HOH HOH . J 5 HOH B 10 410 99 HOH HOH . J 5 HOH B 11 411 100 HOH HOH . J 5 HOH B 12 412 101 HOH HOH . J 5 HOH B 13 413 102 HOH HOH . J 5 HOH B 14 414 103 HOH HOH . J 5 HOH B 15 415 104 HOH HOH . J 5 HOH B 16 416 105 HOH HOH . J 5 HOH B 17 417 106 HOH HOH . J 5 HOH B 18 418 107 HOH HOH . J 5 HOH B 19 419 108 HOH HOH . J 5 HOH B 20 420 109 HOH HOH . J 5 HOH B 21 421 110 HOH HOH . J 5 HOH B 22 422 111 HOH HOH . J 5 HOH B 23 423 112 HOH HOH . J 5 HOH B 24 424 113 HOH HOH . J 5 HOH B 25 425 114 HOH HOH . J 5 HOH B 26 426 115 HOH HOH . J 5 HOH B 27 427 116 HOH HOH . J 5 HOH B 28 428 117 HOH HOH . J 5 HOH B 29 429 118 HOH HOH . J 5 HOH B 30 430 119 HOH HOH . J 5 HOH B 31 431 120 HOH HOH . J 5 HOH B 32 432 121 HOH HOH . J 5 HOH B 33 433 122 HOH HOH . J 5 HOH B 34 434 123 HOH HOH . J 5 HOH B 35 435 124 HOH HOH . J 5 HOH B 36 436 125 HOH HOH . J 5 HOH B 37 437 126 HOH HOH . J 5 HOH B 38 438 127 HOH HOH . J 5 HOH B 39 439 128 HOH HOH . J 5 HOH B 40 440 129 HOH HOH . J 5 HOH B 41 441 130 HOH HOH . J 5 HOH B 42 442 131 HOH HOH . J 5 HOH B 43 443 132 HOH HOH . J 5 HOH B 44 444 133 HOH HOH . J 5 HOH B 45 445 134 HOH HOH . J 5 HOH B 46 446 135 HOH HOH . J 5 HOH B 47 447 136 HOH HOH . J 5 HOH B 48 448 137 HOH HOH . J 5 HOH B 49 449 138 HOH HOH . J 5 HOH B 50 450 139 HOH HOH . J 5 HOH B 51 451 140 HOH HOH . J 5 HOH B 52 452 141 HOH HOH . J 5 HOH B 53 453 142 HOH HOH . J 5 HOH B 54 454 143 HOH HOH . J 5 HOH B 55 455 144 HOH HOH . J 5 HOH B 56 456 145 HOH HOH . J 5 HOH B 57 457 146 HOH HOH . J 5 HOH B 58 458 147 HOH HOH . J 5 HOH B 59 459 148 HOH HOH . J 5 HOH B 60 460 149 HOH HOH . J 5 HOH B 61 461 150 HOH HOH . J 5 HOH B 62 462 151 HOH HOH . J 5 HOH B 63 463 152 HOH HOH . J 5 HOH B 64 464 153 HOH HOH . J 5 HOH B 65 465 154 HOH HOH . J 5 HOH B 66 466 155 HOH HOH . J 5 HOH B 67 467 156 HOH HOH . J 5 HOH B 68 468 157 HOH HOH . J 5 HOH B 69 469 158 HOH HOH . J 5 HOH B 70 470 159 HOH HOH . J 5 HOH B 71 471 160 HOH HOH . J 5 HOH B 72 472 161 HOH HOH . J 5 HOH B 73 473 162 HOH HOH . J 5 HOH B 74 474 163 HOH HOH . J 5 HOH B 75 475 164 HOH HOH . J 5 HOH B 76 476 165 HOH HOH . J 5 HOH B 77 477 166 HOH HOH . J 5 HOH B 78 478 167 HOH HOH . J 5 HOH B 79 479 168 HOH HOH . J 5 HOH B 80 480 169 HOH HOH . J 5 HOH B 81 481 170 HOH HOH . J 5 HOH B 82 482 171 HOH HOH . J 5 HOH B 83 483 172 HOH HOH . J 5 HOH B 84 484 173 HOH HOH . J 5 HOH B 85 485 174 HOH HOH . J 5 HOH B 86 486 175 HOH HOH . J 5 HOH B 87 487 176 HOH HOH . J 5 HOH B 88 488 177 HOH HOH . J 5 HOH B 89 489 178 HOH HOH . J 5 HOH B 90 490 179 HOH HOH . J 5 HOH B 91 491 180 HOH HOH . J 5 HOH B 92 492 183 HOH HOH . J 5 HOH B 93 493 184 HOH HOH . J 5 HOH B 94 494 185 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 UDP . . . H 4 63.64 -9.362 17.025 1 43.24 ? N1 UDP 303 B 1 HETATM 2 C C2 UDP . . . H 4 64.761 -9.396 17.886 1 47.1 ? C2 UDP 303 B 1 HETATM 3 N N3 UDP . . . H 4 64.795 -10.241 18.921 1 46.5 ? N3 UDP 303 B 1 HETATM 4 C C4 UDP . . . H 4 63.781 -11.076 19.17 1 45.6 ? C4 UDP 303 B 1 HETATM 5 C C5 UDP . . . H 4 62.657 -11.075 18.347 1 43.86 ? C5 UDP 303 B 1 HETATM 6 C C6 UDP . . . H 4 62.613 -10.2 17.269 1 43.5 ? C6 UDP 303 B 1 HETATM 7 O O2 UDP . . . H 4 65.731 -8.634 17.69 1 48.49 ? O2 UDP 303 B 1 HETATM 8 O O4 UDP . . . H 4 63.849 -11.851 20.141 1 45.17 ? O4 UDP 303 B 1 HETATM 9 C C1' UDP . . . H 4 63.633 -8.413 15.905 1 41.15 ? C1' UDP 303 B 1 HETATM 10 C C2' UDP . . . H 4 63.49 -9.079 14.545 1 41.34 ? C2' UDP 303 B 1 HETATM 11 O O2' UDP . . . H 4 64.774 -9.338 13.938 1 40.44 ? O2' UDP 303 B 1 HETATM 12 C C3' UDP . . . H 4 62.621 -8.124 13.749 1 41.24 ? C3' UDP 303 B 1 HETATM 13 C C4' UDP . . . H 4 61.857 -7.352 14.826 1 37.19 ? C4' UDP 303 B 1 HETATM 14 O O4' UDP . . . H 4 62.564 -7.473 16.063 1 39.88 ? O4' UDP 303 B 1 HETATM 15 O O3' UDP . . . H 4 63.371 -7.288 12.861 1 44.38 ? O3' UDP 303 B 1 HETATM 16 C C5' UDP . . . H 4 60.443 -7.892 15.058 1 38.32 ? C5' UDP 303 B 1 HETATM 17 O O5' UDP . . . H 4 60.432 -9.317 14.982 1 35.83 ? O5' UDP 303 B 1 HETATM 18 P PA UDP . . . H 4 59.584 -10.045 13.788 1 35.11 ? PA UDP 303 B 1 HETATM 19 O O1A UDP . . . H 4 59.773 -9.325 12.517 1 33.31 ? O1A UDP 303 B 1 HETATM 20 O O2A UDP . . . H 4 59.866 -11.536 13.798 1 34.34 ? O2A UDP 303 B 1 HETATM 21 O O3A UDP . . . H 4 58.115 -9.771 14.394 1 31.61 ? O3A UDP 303 B 1 HETATM 22 P PB UDP . . . H 4 56.641 -10.156 13.785 1 32.84 ? PB UDP 303 B 1 HETATM 23 O O1B UDP . . . H 4 56.728 -11.232 12.734 1 34.13 ? O1B UDP 303 B 1 HETATM 24 O O2B UDP . . . H 4 56.036 -8.861 13.294 1 30.97 ? O2B UDP 303 B 1 HETATM 25 O O3B UDP . . . H 4 55.912 -10.58 15.052 1 28.87 ? O3B UDP 303 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #