data_4JLK # _model_server_result.job_id YPoJrLw78z175rswYtuRSg _model_server_result.datetime_utc '2025-02-27 02:07:11' _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 4jlk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4JLK # _exptl.entry_id 4JLK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 4JLK _cell.length_a 68.6 _cell.length_b 68.6 _cell.length_c 120.706 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JLK _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 ? 2 C N N ? 2 F 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 408 n n N1 C6 UDP sing 409 n n N1 C1' UDP sing 410 n n C2 N3 UDP sing 411 n n C2 O2 UDP doub 412 n n N3 C4 UDP sing 413 n n N3 HN3 UDP sing 414 n n C4 C5 UDP sing 415 n n C4 O4 UDP doub 416 n n C5 C6 UDP doub 417 n n C5 H5 UDP sing 418 n n C6 H6 UDP sing 419 n n C1' C2' UDP sing 420 n n C1' O4' UDP sing 421 n n C1' H1' UDP sing 422 n n C2' O2' UDP sing 423 n n C2' C3' UDP sing 424 n n C2' H2' UDP sing 425 n n O2' HO2' UDP sing 426 n n C3' C4' UDP sing 427 n n C3' O3' UDP sing 428 n n C3' H3' UDP sing 429 n n C4' O4' UDP sing 430 n n C4' C5' UDP sing 431 n n C4' H4' UDP sing 432 n n O3' HO3' UDP sing 433 n n C5' O5' UDP sing 434 n n C5' "H5'1" UDP sing 435 n n C5' "H5'2" UDP sing 436 n n O5' PA UDP sing 437 n n PA O1A UDP doub 438 n n PA O2A UDP sing 439 n n PA O3A UDP sing 440 n n O2A HOA2 UDP sing 441 n n O3A PB UDP sing 442 n n PB O1B UDP doub 443 n n PB O2B UDP sing 444 n n PB O3B UDP sing 445 n n O2B HOB2 UDP sing 446 n n O3B HOB3 UDP sing 447 n n # _atom_sites.entry_id 4JLK _atom_sites.fract_transf_matrix[1][1] 0.014577 _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] 0.014577 _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] 0.008285 _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 UDP A 1 401 401 UDP UDP . D 3 1NO A 1 402 301 1NO DRG . E 3 1NO A 1 403 302 1NO DRG . F 2 UDP B 1 401 401 UDP UDP . G 3 1NO B 1 402 301 1NO DRG . H 3 1NO B 1 403 302 1NO DRG . I 4 HOH A 1 501 2 HOH HOH . I 4 HOH A 2 502 3 HOH HOH . I 4 HOH A 3 503 4 HOH HOH . I 4 HOH A 4 504 7 HOH HOH . I 4 HOH A 5 505 8 HOH HOH . I 4 HOH A 6 506 9 HOH HOH . I 4 HOH A 7 507 17 HOH HOH . I 4 HOH A 8 508 23 HOH HOH . I 4 HOH A 9 509 25 HOH HOH . I 4 HOH A 10 510 28 HOH HOH . I 4 HOH A 11 511 31 HOH HOH . I 4 HOH A 12 512 33 HOH HOH . I 4 HOH A 13 513 36 HOH HOH . I 4 HOH A 14 514 38 HOH HOH . I 4 HOH A 15 515 39 HOH HOH . I 4 HOH A 16 516 40 HOH HOH . I 4 HOH A 17 517 41 HOH HOH . I 4 HOH A 18 518 43 HOH HOH . I 4 HOH A 19 519 45 HOH HOH . I 4 HOH A 20 520 48 HOH HOH . I 4 HOH A 21 521 49 HOH HOH . I 4 HOH A 22 522 50 HOH HOH . I 4 HOH A 23 523 53 HOH HOH . I 4 HOH A 24 524 54 HOH HOH . I 4 HOH A 25 525 56 HOH HOH . I 4 HOH A 26 526 62 HOH HOH . I 4 HOH A 27 527 65 HOH HOH . I 4 HOH A 28 528 66 HOH HOH . I 4 HOH A 29 529 67 HOH HOH . I 4 HOH A 30 530 68 HOH HOH . I 4 HOH A 31 531 69 HOH HOH . I 4 HOH A 32 532 70 HOH HOH . I 4 HOH A 33 533 71 HOH HOH . I 4 HOH A 34 534 72 HOH HOH . I 4 HOH A 35 535 74 HOH HOH . I 4 HOH A 36 536 76 HOH HOH . I 4 HOH A 37 537 78 HOH HOH . I 4 HOH A 38 538 79 HOH HOH . I 4 HOH A 39 539 81 HOH HOH . I 4 HOH A 40 540 82 HOH HOH . I 4 HOH A 41 541 83 HOH HOH . I 4 HOH A 42 542 88 HOH HOH . I 4 HOH A 43 543 89 HOH HOH . I 4 HOH A 44 544 91 HOH HOH . I 4 HOH A 45 545 94 HOH HOH . I 4 HOH A 46 546 95 HOH HOH . I 4 HOH A 47 547 97 HOH HOH . I 4 HOH A 48 548 98 HOH HOH . I 4 HOH A 49 549 99 HOH HOH . I 4 HOH A 50 550 100 HOH HOH . I 4 HOH A 51 551 103 HOH HOH . I 4 HOH A 52 552 106 HOH HOH . I 4 HOH A 53 553 108 HOH HOH . I 4 HOH A 54 554 109 HOH HOH . I 4 HOH A 55 555 112 HOH HOH . I 4 HOH A 56 556 113 HOH HOH . I 4 HOH A 57 557 117 HOH HOH . I 4 HOH A 58 558 119 HOH HOH . I 4 HOH A 59 559 120 HOH HOH . I 4 HOH A 60 560 123 HOH HOH . I 4 HOH A 61 561 125 HOH HOH . I 4 HOH A 62 562 127 HOH HOH . I 4 HOH A 63 563 132 HOH HOH . I 4 HOH A 64 564 135 HOH HOH . I 4 HOH A 65 565 137 HOH HOH . I 4 HOH A 66 566 139 HOH HOH . I 4 HOH A 67 567 140 HOH HOH . I 4 HOH A 68 568 141 HOH HOH . I 4 HOH A 69 569 142 HOH HOH . I 4 HOH A 70 570 145 HOH HOH . I 4 HOH A 71 571 147 HOH HOH . I 4 HOH A 72 572 148 HOH HOH . I 4 HOH A 73 573 149 HOH HOH . I 4 HOH A 74 574 150 HOH HOH . I 4 HOH A 75 575 153 HOH HOH . I 4 HOH A 76 576 156 HOH HOH . I 4 HOH A 77 577 157 HOH HOH . I 4 HOH A 78 578 159 HOH HOH . I 4 HOH A 79 579 160 HOH HOH . I 4 HOH A 80 580 163 HOH HOH . I 4 HOH A 81 581 164 HOH HOH . I 4 HOH A 82 582 166 HOH HOH . I 4 HOH A 83 583 167 HOH HOH . I 4 HOH A 84 584 169 HOH HOH . I 4 HOH A 85 585 170 HOH HOH . I 4 HOH A 86 586 173 HOH HOH . I 4 HOH A 87 587 174 HOH HOH . I 4 HOH A 88 588 176 HOH HOH . I 4 HOH A 89 589 177 HOH HOH . I 4 HOH A 90 590 182 HOH HOH . I 4 HOH A 91 591 185 HOH HOH . I 4 HOH A 92 592 186 HOH HOH . I 4 HOH A 93 593 191 HOH HOH . I 4 HOH A 94 594 196 HOH HOH . I 4 HOH A 95 595 197 HOH HOH . I 4 HOH A 96 596 198 HOH HOH . I 4 HOH A 97 597 199 HOH HOH . I 4 HOH A 98 598 200 HOH HOH . I 4 HOH A 99 599 206 HOH HOH . I 4 HOH A 100 600 208 HOH HOH . J 4 HOH B 1 501 1 HOH HOH . J 4 HOH B 2 502 5 HOH HOH . J 4 HOH B 3 503 6 HOH HOH . J 4 HOH B 4 504 10 HOH HOH . J 4 HOH B 5 505 11 HOH HOH . J 4 HOH B 6 506 12 HOH HOH . J 4 HOH B 7 507 13 HOH HOH . J 4 HOH B 8 508 14 HOH HOH . J 4 HOH B 9 509 15 HOH HOH . J 4 HOH B 10 510 16 HOH HOH . J 4 HOH B 11 511 18 HOH HOH . J 4 HOH B 12 512 19 HOH HOH . J 4 HOH B 13 513 20 HOH HOH . J 4 HOH B 14 514 21 HOH HOH . J 4 HOH B 15 515 22 HOH HOH . J 4 HOH B 16 516 24 HOH HOH . J 4 HOH B 17 517 26 HOH HOH . J 4 HOH B 18 518 27 HOH HOH . J 4 HOH B 19 519 29 HOH HOH . J 4 HOH B 20 520 30 HOH HOH . J 4 HOH B 21 521 32 HOH HOH . J 4 HOH B 22 522 34 HOH HOH . J 4 HOH B 23 523 35 HOH HOH . J 4 HOH B 24 524 37 HOH HOH . J 4 HOH B 25 525 42 HOH HOH . J 4 HOH B 26 526 44 HOH HOH . J 4 HOH B 27 527 46 HOH HOH . J 4 HOH B 28 528 47 HOH HOH . J 4 HOH B 29 529 51 HOH HOH . J 4 HOH B 30 530 52 HOH HOH . J 4 HOH B 31 531 55 HOH HOH . J 4 HOH B 32 532 57 HOH HOH . J 4 HOH B 33 533 58 HOH HOH . J 4 HOH B 34 534 59 HOH HOH . J 4 HOH B 35 535 60 HOH HOH . J 4 HOH B 36 536 61 HOH HOH . J 4 HOH B 37 537 63 HOH HOH . J 4 HOH B 38 538 64 HOH HOH . J 4 HOH B 39 539 73 HOH HOH . J 4 HOH B 40 540 75 HOH HOH . J 4 HOH B 41 541 77 HOH HOH . J 4 HOH B 42 542 80 HOH HOH . J 4 HOH B 43 543 84 HOH HOH . J 4 HOH B 44 544 85 HOH HOH . J 4 HOH B 45 545 86 HOH HOH . J 4 HOH B 46 546 87 HOH HOH . J 4 HOH B 47 547 90 HOH HOH . J 4 HOH B 48 548 92 HOH HOH . J 4 HOH B 49 549 93 HOH HOH . J 4 HOH B 50 550 96 HOH HOH . J 4 HOH B 51 551 101 HOH HOH . J 4 HOH B 52 552 102 HOH HOH . J 4 HOH B 53 553 104 HOH HOH . J 4 HOH B 54 554 105 HOH HOH . J 4 HOH B 55 555 107 HOH HOH . J 4 HOH B 56 556 110 HOH HOH . J 4 HOH B 57 557 111 HOH HOH . J 4 HOH B 58 558 114 HOH HOH . J 4 HOH B 59 559 115 HOH HOH . J 4 HOH B 60 560 116 HOH HOH . J 4 HOH B 61 561 118 HOH HOH . J 4 HOH B 62 562 121 HOH HOH . J 4 HOH B 63 563 122 HOH HOH . J 4 HOH B 64 564 124 HOH HOH . J 4 HOH B 65 565 126 HOH HOH . J 4 HOH B 66 566 128 HOH HOH . J 4 HOH B 67 567 129 HOH HOH . J 4 HOH B 68 568 130 HOH HOH . J 4 HOH B 69 569 131 HOH HOH . J 4 HOH B 70 570 133 HOH HOH . J 4 HOH B 71 571 134 HOH HOH . J 4 HOH B 72 572 136 HOH HOH . J 4 HOH B 73 573 138 HOH HOH . J 4 HOH B 74 574 143 HOH HOH . J 4 HOH B 75 575 144 HOH HOH . J 4 HOH B 76 576 146 HOH HOH . J 4 HOH B 77 577 151 HOH HOH . J 4 HOH B 78 578 152 HOH HOH . J 4 HOH B 79 579 154 HOH HOH . J 4 HOH B 80 580 155 HOH HOH . J 4 HOH B 81 581 158 HOH HOH . J 4 HOH B 82 582 161 HOH HOH . J 4 HOH B 83 583 162 HOH HOH . J 4 HOH B 84 584 165 HOH HOH . J 4 HOH B 85 585 168 HOH HOH . J 4 HOH B 86 586 171 HOH HOH . J 4 HOH B 87 587 172 HOH HOH . J 4 HOH B 88 588 175 HOH HOH . J 4 HOH B 89 589 178 HOH HOH . J 4 HOH B 90 590 179 HOH HOH . J 4 HOH B 91 591 180 HOH HOH . J 4 HOH B 92 592 181 HOH HOH . J 4 HOH B 93 593 183 HOH HOH . J 4 HOH B 94 594 184 HOH HOH . J 4 HOH B 95 595 187 HOH HOH . J 4 HOH B 96 596 188 HOH HOH . J 4 HOH B 97 597 189 HOH HOH . J 4 HOH B 98 598 190 HOH HOH . J 4 HOH B 99 599 192 HOH HOH . J 4 HOH B 100 600 193 HOH HOH . J 4 HOH B 101 601 194 HOH HOH . J 4 HOH B 102 602 195 HOH HOH . J 4 HOH B 103 603 201 HOH HOH . J 4 HOH B 104 604 202 HOH HOH . J 4 HOH B 105 605 203 HOH HOH . J 4 HOH B 106 606 204 HOH HOH . J 4 HOH B 107 607 205 HOH HOH . J 4 HOH B 108 608 207 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 . . . C 2 -25.333 28.612 4.312 1 40.98 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . C 2 -25.135 29.862 4.976 1 43.48 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . C 2 -24.096 30.041 5.799 1 44.25 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . C 2 -23.22 29.048 5.994 1 44.23 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . C 2 -23.377 27.803 5.354 1 41.12 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . C 2 -24.458 27.603 4.501 1 40.47 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . C 2 -25.932 30.814 4.818 1 49.82 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . C 2 -22.256 29.254 6.757 1 43.91 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . C 2 -26.478 28.459 3.4 1 39.44 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . C 2 -26.051 28.499 1.935 1 38.52 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . C 2 -25.947 29.806 1.342 1 43.49 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . C 2 -27.145 27.697 1.268 1 40.02 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . C 2 -27.533 26.672 2.311 1 39.38 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . C 2 -27.113 27.191 3.568 1 37.76 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . C 2 -28.26 28.541 1.004 1 33.9 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . C 2 -26.803 25.359 2.061 1 39.78 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . C 2 -25.397 25.59 1.873 1 37.8 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . C 2 -24.587 24.634 0.853 1 38.88 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . C 2 -25.091 24.643 -0.566 1 34.96 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . C 2 -23.135 25.013 1.008 1 36.34 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . C 2 -24.941 23.199 1.53 1 32.88 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . C 2 -24.411 21.768 0.991 1 31.5 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . C 2 -23.372 22.128 -0.017 1 27.29 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . C 2 -25.611 21.102 0.332 1 33.52 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . C 2 -23.942 21.048 2.251 1 31.5 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 25 #