data_5HVO # _model_server_result.job_id ktpSybWRA8jNqaAqYqWunA _model_server_result.datetime_utc '2024-11-08 17:38:51' _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 5hvo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 5HVO # _exptl.entry_id 5HVO _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 4 _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 5HVO _cell.length_a 88.276 _cell.length_b 130.581 _cell.length_c 184.813 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HVO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 2 21 21' # 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 PISA tetrameric 4 software_defined_assembly 3 PISA tetrameric 4 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 1 A,B,E,F,G,H,M,N 3 1,2 C,D,I,J,K,L,O,P 4 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 130.581 0 3 'crystal symmetry operation' 2_564 x,-y+1,-z-1 1 0 0 0 -1 0 0 0 -1 0 130.581 -184.813 # 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 G N N ? 2 I N N ? 2 K 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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 5HVO _atom_sites.fract_transf_matrix[1][1] 0.011328 _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] 0.007658 _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] 0.005411 _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 UDP A 1 501 501 UDP UDP . F 3 VDM A 1 502 502 VDM VDM . G 2 UDP B 1 501 501 UDP UDP . H 3 VDM B 1 502 502 VDM VDM . I 2 UDP C 1 501 501 UDP UDP . J 3 VDM C 1 502 502 VDM VDM . K 2 UDP D 1 501 501 UDP UDP . L 3 VDM D 1 502 502 VDM VDM . M 4 HOH A 1 601 49 HOH HOH . M 4 HOH A 2 602 21 HOH HOH . M 4 HOH A 3 603 52 HOH HOH . M 4 HOH A 4 604 10 HOH HOH . M 4 HOH A 5 605 86 HOH HOH . M 4 HOH A 6 606 119 HOH HOH . M 4 HOH A 7 607 83 HOH HOH . M 4 HOH A 8 608 146 HOH HOH . M 4 HOH A 9 609 5 HOH HOH . M 4 HOH A 10 610 41 HOH HOH . M 4 HOH A 11 611 142 HOH HOH . M 4 HOH A 12 612 40 HOH HOH . M 4 HOH A 13 613 148 HOH HOH . M 4 HOH A 14 614 20 HOH HOH . M 4 HOH A 15 615 112 HOH HOH . M 4 HOH A 16 616 62 HOH HOH . M 4 HOH A 17 617 7 HOH HOH . M 4 HOH A 18 618 139 HOH HOH . M 4 HOH A 19 619 75 HOH HOH . M 4 HOH A 20 620 73 HOH HOH . M 4 HOH A 21 621 69 HOH HOH . M 4 HOH A 22 622 17 HOH HOH . M 4 HOH A 23 623 25 HOH HOH . M 4 HOH A 24 624 31 HOH HOH . M 4 HOH A 25 625 29 HOH HOH . M 4 HOH A 26 626 19 HOH HOH . M 4 HOH A 27 627 37 HOH HOH . M 4 HOH A 28 628 28 HOH HOH . M 4 HOH A 29 629 167 HOH HOH . M 4 HOH A 30 630 33 HOH HOH . M 4 HOH A 31 631 110 HOH HOH . M 4 HOH A 32 632 181 HOH HOH . M 4 HOH A 33 633 144 HOH HOH . M 4 HOH A 34 634 88 HOH HOH . M 4 HOH A 35 635 14 HOH HOH . M 4 HOH A 36 636 38 HOH HOH . M 4 HOH A 37 637 81 HOH HOH . M 4 HOH A 38 638 90 HOH HOH . M 4 HOH A 39 639 149 HOH HOH . M 4 HOH A 40 640 176 HOH HOH . M 4 HOH A 41 641 185 HOH HOH . M 4 HOH A 42 642 96 HOH HOH . M 4 HOH A 43 643 168 HOH HOH . M 4 HOH A 44 644 107 HOH HOH . M 4 HOH A 45 645 51 HOH HOH . M 4 HOH A 46 646 136 HOH HOH . M 4 HOH A 47 647 191 HOH HOH . M 4 HOH A 48 648 84 HOH HOH . M 4 HOH A 49 649 34 HOH HOH . M 4 HOH A 50 650 85 HOH HOH . M 4 HOH A 51 651 192 HOH HOH . N 4 HOH B 1 601 177 HOH HOH . N 4 HOH B 2 602 132 HOH HOH . N 4 HOH B 3 603 174 HOH HOH . N 4 HOH B 4 604 48 HOH HOH . N 4 HOH B 5 605 116 HOH HOH . N 4 HOH B 6 606 65 HOH HOH . N 4 HOH B 7 607 50 HOH HOH . N 4 HOH B 8 608 99 HOH HOH . N 4 HOH B 9 609 47 HOH HOH . N 4 HOH B 10 610 89 HOH HOH . N 4 HOH B 11 611 61 HOH HOH . N 4 HOH B 12 612 1 HOH HOH . N 4 HOH B 13 613 159 HOH HOH . N 4 HOH B 14 614 104 HOH HOH . N 4 HOH B 15 615 183 HOH HOH . N 4 HOH B 16 616 70 HOH HOH . N 4 HOH B 17 617 16 HOH HOH . N 4 HOH B 18 618 32 HOH HOH . N 4 HOH B 19 619 78 HOH HOH . N 4 HOH B 20 620 82 HOH HOH . N 4 HOH B 21 621 156 HOH HOH . N 4 HOH B 22 622 106 HOH HOH . N 4 HOH B 23 623 24 HOH HOH . N 4 HOH B 24 624 150 HOH HOH . N 4 HOH B 25 625 123 HOH HOH . N 4 HOH B 26 626 91 HOH HOH . N 4 HOH B 27 627 11 HOH HOH . N 4 HOH B 28 628 53 HOH HOH . N 4 HOH B 29 629 35 HOH HOH . N 4 HOH B 30 630 160 HOH HOH . N 4 HOH B 31 631 66 HOH HOH . N 4 HOH B 32 632 137 HOH HOH . N 4 HOH B 33 633 43 HOH HOH . N 4 HOH B 34 634 100 HOH HOH . N 4 HOH B 35 635 74 HOH HOH . N 4 HOH B 36 636 153 HOH HOH . N 4 HOH B 37 637 122 HOH HOH . N 4 HOH B 38 638 39 HOH HOH . N 4 HOH B 39 639 147 HOH HOH . N 4 HOH B 40 640 171 HOH HOH . N 4 HOH B 41 641 180 HOH HOH . N 4 HOH B 42 642 121 HOH HOH . N 4 HOH B 43 643 103 HOH HOH . N 4 HOH B 44 644 172 HOH HOH . N 4 HOH B 45 645 105 HOH HOH . O 4 HOH C 1 601 157 HOH HOH . O 4 HOH C 2 602 118 HOH HOH . O 4 HOH C 3 603 55 HOH HOH . O 4 HOH C 4 604 4 HOH HOH . O 4 HOH C 5 605 18 HOH HOH . O 4 HOH C 6 606 173 HOH HOH . O 4 HOH C 7 607 27 HOH HOH . O 4 HOH C 8 608 44 HOH HOH . O 4 HOH C 9 609 76 HOH HOH . O 4 HOH C 10 610 77 HOH HOH . O 4 HOH C 11 611 8 HOH HOH . O 4 HOH C 12 612 94 HOH HOH . O 4 HOH C 13 613 130 HOH HOH . O 4 HOH C 14 614 64 HOH HOH . O 4 HOH C 15 615 15 HOH HOH . O 4 HOH C 16 616 36 HOH HOH . O 4 HOH C 17 617 59 HOH HOH . O 4 HOH C 18 618 30 HOH HOH . O 4 HOH C 19 619 87 HOH HOH . O 4 HOH C 20 620 170 HOH HOH . O 4 HOH C 21 621 165 HOH HOH . O 4 HOH C 22 622 42 HOH HOH . O 4 HOH C 23 623 115 HOH HOH . O 4 HOH C 24 624 128 HOH HOH . O 4 HOH C 25 625 190 HOH HOH . O 4 HOH C 26 626 163 HOH HOH . O 4 HOH C 27 627 57 HOH HOH . O 4 HOH C 28 628 151 HOH HOH . O 4 HOH C 29 629 161 HOH HOH . O 4 HOH C 30 630 97 HOH HOH . O 4 HOH C 31 631 135 HOH HOH . O 4 HOH C 32 632 178 HOH HOH . O 4 HOH C 33 633 143 HOH HOH . O 4 HOH C 34 634 26 HOH HOH . O 4 HOH C 35 635 138 HOH HOH . O 4 HOH C 36 636 186 HOH HOH . O 4 HOH C 37 637 60 HOH HOH . O 4 HOH C 38 638 155 HOH HOH . O 4 HOH C 39 639 182 HOH HOH . O 4 HOH C 40 640 188 HOH HOH . O 4 HOH C 41 641 169 HOH HOH . O 4 HOH C 42 642 179 HOH HOH . P 4 HOH D 1 601 98 HOH HOH . P 4 HOH D 2 602 23 HOH HOH . P 4 HOH D 3 603 2 HOH HOH . P 4 HOH D 4 604 134 HOH HOH . P 4 HOH D 5 605 71 HOH HOH . P 4 HOH D 6 606 140 HOH HOH . P 4 HOH D 7 607 67 HOH HOH . P 4 HOH D 8 608 125 HOH HOH . P 4 HOH D 9 609 6 HOH HOH . P 4 HOH D 10 610 108 HOH HOH . P 4 HOH D 11 611 158 HOH HOH . P 4 HOH D 12 612 68 HOH HOH . P 4 HOH D 13 613 154 HOH HOH . P 4 HOH D 14 614 46 HOH HOH . P 4 HOH D 15 615 133 HOH HOH . P 4 HOH D 16 616 95 HOH HOH . P 4 HOH D 17 617 141 HOH HOH . P 4 HOH D 18 618 109 HOH HOH . P 4 HOH D 19 619 3 HOH HOH . P 4 HOH D 20 620 127 HOH HOH . P 4 HOH D 21 621 72 HOH HOH . P 4 HOH D 22 622 63 HOH HOH . P 4 HOH D 23 623 189 HOH HOH . P 4 HOH D 24 624 184 HOH HOH . P 4 HOH D 25 625 9 HOH HOH . P 4 HOH D 26 626 79 HOH HOH . P 4 HOH D 27 627 124 HOH HOH . P 4 HOH D 28 628 56 HOH HOH . P 4 HOH D 29 629 93 HOH HOH . P 4 HOH D 30 630 13 HOH HOH . P 4 HOH D 31 631 54 HOH HOH . P 4 HOH D 32 632 102 HOH HOH . P 4 HOH D 33 633 175 HOH HOH . P 4 HOH D 34 634 129 HOH HOH . P 4 HOH D 35 635 126 HOH HOH . P 4 HOH D 36 636 117 HOH HOH . P 4 HOH D 37 637 162 HOH HOH . P 4 HOH D 38 638 114 HOH HOH . P 4 HOH D 39 639 131 HOH HOH . P 4 HOH D 40 640 187 HOH HOH . P 4 HOH D 41 641 58 HOH HOH . P 4 HOH D 42 642 80 HOH HOH . P 4 HOH D 43 643 113 HOH HOH . P 4 HOH D 44 644 111 HOH HOH . P 4 HOH D 45 645 120 HOH HOH . P 4 HOH D 46 646 166 HOH HOH . P 4 HOH D 47 647 12 HOH HOH . P 4 HOH D 48 648 101 HOH HOH . P 4 HOH D 49 649 22 HOH HOH . P 4 HOH D 50 650 45 HOH HOH . P 4 HOH D 51 651 152 HOH HOH . P 4 HOH D 52 652 145 HOH HOH . P 4 HOH D 53 653 92 HOH HOH . P 4 HOH D 54 654 164 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 . . . K 2 -6.137 87.697 -76.102 1 43.3 ? N1 UDP 501 D 1 HETATM 2 C C2 UDP . . . K 2 -5.057 87.116 -76.897 1 43.08 ? C2 UDP 501 D 1 HETATM 3 N N3 UDP . . . K 2 -4.967 87.353 -78.337 1 45.47 ? N3 UDP 501 D 1 HETATM 4 C C4 UDP . . . K 2 -5.92 88.173 -78.987 1 45.14 ? C4 UDP 501 D 1 HETATM 5 C C5 UDP . . . K 2 -7.012 88.775 -78.215 1 40.32 ? C5 UDP 501 D 1 HETATM 6 C C6 UDP . . . K 2 -7.097 88.528 -76.762 1 46.01 ? C6 UDP 501 D 1 HETATM 7 O O2 UDP . . . K 2 -4.226 86.42 -76.359 1 51.33 ? O2 UDP 501 D 1 HETATM 8 O O4 UDP . . . K 2 -5.827 88.364 -80.182 1 50.21 ? O4 UDP 501 D 1 HETATM 9 C C1' UDP . . . K 2 -6.156 87.464 -74.716 1 43.75 ? C1' UDP 501 D 1 HETATM 10 C C2' UDP . . . K 2 -7.179 88.04 -74.088 1 46.95 ? C2' UDP 501 D 1 HETATM 11 O O2' UDP . . . K 2 -6.918 89.476 -73.881 1 48.83 ? O2' UDP 501 D 1 HETATM 12 C C3' UDP . . . K 2 -7.239 87.281 -72.738 1 47.51 ? C3' UDP 501 D 1 HETATM 13 C C4' UDP . . . K 2 -6.733 85.825 -73.118 1 42.1 ? C4' UDP 501 D 1 HETATM 14 O O4' UDP . . . K 2 -6.295 85.892 -74.343 1 44.91 ? O4' UDP 501 D 1 HETATM 15 O O3' UDP . . . K 2 -6.453 87.843 -71.821 1 41.7 ? O3' UDP 501 D 1 HETATM 16 C C5' UDP . . . K 2 -7.891 84.848 -73.037 1 37.09 ? C5' UDP 501 D 1 HETATM 17 O O5' UDP . . . K 2 -8 84.534 -71.691 1 32.48 ? O5' UDP 501 D 1 HETATM 18 P PA UDP . . . K 2 -9.224 83.789 -71.036 1 40.55 ? PA UDP 501 D 1 HETATM 19 O O1A UDP . . . K 2 -10.508 84.595 -71.109 1 37.5 ? O1A UDP 501 D 1 HETATM 20 O O2A UDP . . . K 2 -8.882 83.543 -69.58 1 38.34 ? O2A UDP 501 D 1 HETATM 21 O O3A UDP . . . K 2 -9.48 82.386 -71.728 1 44.27 ? O3A UDP 501 D 1 HETATM 22 P PB UDP . . . K 2 -8.428 81.326 -72.211 1 39.77 ? PB UDP 501 D 1 HETATM 23 O O1B UDP . . . K 2 -7.906 81.665 -73.591 1 35.55 ? O1B UDP 501 D 1 HETATM 24 O O2B UDP . . . K 2 -9.185 80.023 -72.225 1 41.14 ? O2B UDP 501 D 1 HETATM 25 O O3B UDP . . . K 2 -7.255 81.229 -71.264 1 41.34 ? O3B UDP 501 D 1 HETATM 26 H HN3 UDP . . . K 2 -4.288 86.979 -78.817 1 54.56 ? HN3 UDP 501 D 1 HETATM 27 H H5 UDP . . . K 2 -7.674 89.339 -78.658 1 48.39 ? H5 UDP 501 D 1 HETATM 28 H H6 UDP . . . K 2 -7.818 88.935 -76.246 1 55.22 ? H6 UDP 501 D 1 HETATM 29 H H1' UDP . . . K 2 -5.322 87.804 -74.332 1 52.5 ? H1' UDP 501 D 1 HETATM 30 H H2' UDP . . . K 2 -8.008 87.91 -74.591 1 56.33 ? H2' UDP 501 D 1 HETATM 31 H HO2' UDP . . . K 2 -6.474 89.801 -74.579 1 58.59 ? HO2' UDP 501 D 1 HETATM 32 H H3' UDP . . . K 2 -8.161 87.243 -72.414 1 57.01 ? H3' UDP 501 D 1 HETATM 33 H H4' UDP . . . K 2 -6.013 85.549 -72.515 1 50.52 ? H4' UDP 501 D 1 HETATM 34 H HO3' UDP . . . K 2 -6.824 88.602 -71.537 1 50.04 ? HO3' UDP 501 D 1 HETATM 35 H "H5'1" UDP . . . K 2 -8.714 85.27 -73.357 1 44.51 ? "H5'1" UDP 501 D 1 HETATM 36 H "H5'2" UDP . . . K 2 -7.69 84.044 -73.559 1 44.51 ? "H5'2" UDP 501 D 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #