data_5HVO # _model_server_result.job_id l8oOPpkyNlvYhhkChl96EQ _model_server_result.datetime_utc '2024-11-08 17:45:14' _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":"G","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 . . . G 2 -0.913 79.117 -16.974 1 45.95 ? N1 UDP 501 B 1 HETATM 2 C C2 UDP . . . G 2 -1.541 80.232 -16.256 1 46.24 ? C2 UDP 501 B 1 HETATM 3 N N3 UDP . . . G 2 -1.344 80.417 -14.819 1 47.48 ? N3 UDP 501 B 1 HETATM 4 C C4 UDP . . . G 2 -0.526 79.517 -14.098 1 46.35 ? C4 UDP 501 B 1 HETATM 5 C C5 UDP . . . G 2 0.105 78.397 -14.803 1 43.8 ? C5 UDP 501 B 1 HETATM 6 C C6 UDP . . . G 2 -0.097 78.209 -16.248 1 46.78 ? C6 UDP 501 B 1 HETATM 7 O O2 UDP . . . G 2 -2.241 81.013 -16.861 1 47.73 ? O2 UDP 501 B 1 HETATM 8 O O4 UDP . . . G 2 -0.35 79.676 -12.902 1 48.84 ? O4 UDP 501 B 1 HETATM 9 C C1' UDP . . . G 2 -1.127 79.008 -18.356 1 45.87 ? C1' UDP 501 B 1 HETATM 10 C C2' UDP . . . G 2 -0.495 78.006 -18.966 1 49.89 ? C2' UDP 501 B 1 HETATM 11 O O2' UDP . . . G 2 0.938 78.28 -19.186 1 50 ? O2' UDP 501 B 1 HETATM 12 C C3' UDP . . . G 2 -1.25 77.95 -20.317 1 48.94 ? C3' UDP 501 B 1 HETATM 13 C C4' UDP . . . G 2 -2.728 78.324 -19.921 1 45.94 ? C4' UDP 501 B 1 HETATM 14 O O4' UDP . . . G 2 -2.685 78.721 -18.685 1 46.14 ? O4' UDP 501 B 1 HETATM 15 O O3' UDP . . . G 2 -0.819 78.846 -21.196 1 49.2 ? O3' UDP 501 B 1 HETATM 16 C C5' UDP . . . G 2 -3.6 77.092 -20.069 1 42.61 ? C5' UDP 501 B 1 HETATM 17 O O5' UDP . . . G 2 -4.276 77.277 -21.275 1 38.01 ? O5' UDP 501 B 1 HETATM 18 P PA UDP . . . G 2 -4.847 76.033 -22.065 1 42.24 ? PA UDP 501 B 1 HETATM 19 O O1A UDP . . . G 2 -4.989 76.478 -23.497 1 42.31 ? O1A UDP 501 B 1 HETATM 20 O O2A UDP . . . G 2 -3.907 74.841 -22.015 1 35.15 ? O2A UDP 501 B 1 HETATM 21 O O3A UDP . . . G 2 -6.262 75.719 -21.395 1 36.58 ? O3A UDP 501 B 1 HETATM 22 P PB UDP . . . G 2 -7.308 76.808 -20.894 1 39.17 ? PB UDP 501 B 1 HETATM 23 O O1B UDP . . . G 2 -7.373 77.983 -21.839 1 34.34 ? O1B UDP 501 B 1 HETATM 24 O O2B UDP . . . G 2 -8.66 76.147 -20.824 1 40.66 ? O2B UDP 501 B 1 HETATM 25 O O3B UDP . . . G 2 -6.956 77.355 -19.521 1 43.06 ? O3B UDP 501 B 1 HETATM 26 H HN3 UDP . . . G 2 -1.741 81.118 -14.39 1 56.98 ? HN3 UDP 501 B 1 HETATM 27 H H5 UDP . . . G 2 0.672 77.774 -14.309 1 52.56 ? H5 UDP 501 B 1 HETATM 28 H H6 UDP . . . G 2 0.337 77.466 -16.709 1 56.14 ? H6 UDP 501 B 1 HETATM 29 H H1' UDP . . . G 2 -0.865 79.85 -18.781 1 55.05 ? H1' UDP 501 B 1 HETATM 30 H H2' UDP . . . G 2 -0.615 77.172 -18.47 1 59.87 ? H2' UDP 501 B 1 HETATM 31 H HO2' UDP . . . G 2 1.348 78.365 -18.402 1 60 ? HO2' UDP 501 B 1 HETATM 32 H H3' UDP . . . G 2 -1.213 77.049 -20.695 1 58.73 ? H3' UDP 501 B 1 HETATM 33 H H4' UDP . . . G 2 -3.059 79.044 -20.494 1 55.13 ? H4' UDP 501 B 1 HETATM 34 H HO3' UDP . . . G 2 -0.027 78.592 -21.514 1 59.04 ? HO3' UDP 501 B 1 HETATM 35 H "H5'1" UDP . . . G 2 -3.047 76.286 -20.106 1 51.14 ? "H5'1" UDP 501 B 1 HETATM 36 H "H5'2" UDP . . . G 2 -4.236 77.04 -19.326 1 51.14 ? "H5'2" UDP 501 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #