data_4ORO # _model_server_result.job_id bgIFssxECThK5hQAyRPCgw _model_server_result.datetime_utc '2024-11-29 22:23:41' _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 4oro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 4ORO # _exptl.entry_id 4ORO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 90.08 _cell.angle_gamma 90 _cell.entry_id 4ORO _cell.length_a 83.42 _cell.length_b 42.771 _cell.length_c 118.414 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ORO _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_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,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 4ORO _atom_sites.fract_transf_matrix[1][1] 0.011988 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000017 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02338 _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] 0.008445 _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 GDP A 1 501 1 GDP GDP . F 2 GDP B 1 501 1 GDP GDP . G 2 GDP C 1 501 1 GDP GDP . H 2 GDP D 1 501 1 GDP GDP . I 3 HOH A 1 601 6 HOH HOH . I 3 HOH A 2 602 15 HOH HOH . I 3 HOH A 3 603 19 HOH HOH . I 3 HOH A 4 604 20 HOH HOH . I 3 HOH A 5 605 22 HOH HOH . I 3 HOH A 6 606 26 HOH HOH . I 3 HOH A 7 607 28 HOH HOH . I 3 HOH A 8 608 29 HOH HOH . I 3 HOH A 9 609 30 HOH HOH . I 3 HOH A 10 610 32 HOH HOH . I 3 HOH A 11 611 35 HOH HOH . I 3 HOH A 12 612 38 HOH HOH . I 3 HOH A 13 613 39 HOH HOH . I 3 HOH A 14 614 40 HOH HOH . I 3 HOH A 15 615 46 HOH HOH . I 3 HOH A 16 616 51 HOH HOH . I 3 HOH A 17 617 52 HOH HOH . I 3 HOH A 18 618 55 HOH HOH . I 3 HOH A 19 619 60 HOH HOH . I 3 HOH A 20 620 63 HOH HOH . I 3 HOH A 21 621 70 HOH HOH . I 3 HOH A 22 622 72 HOH HOH . I 3 HOH A 23 623 73 HOH HOH . I 3 HOH A 24 624 77 HOH HOH . I 3 HOH A 25 625 78 HOH HOH . I 3 HOH A 26 626 85 HOH HOH . I 3 HOH A 27 627 87 HOH HOH . I 3 HOH A 28 628 90 HOH HOH . I 3 HOH A 29 629 91 HOH HOH . I 3 HOH A 30 630 103 HOH HOH . I 3 HOH A 31 631 104 HOH HOH . I 3 HOH A 32 632 106 HOH HOH . I 3 HOH A 33 633 109 HOH HOH . I 3 HOH A 34 634 115 HOH HOH . I 3 HOH A 35 635 117 HOH HOH . I 3 HOH A 36 636 123 HOH HOH . I 3 HOH A 37 637 126 HOH HOH . I 3 HOH A 38 638 128 HOH HOH . I 3 HOH A 39 639 130 HOH HOH . I 3 HOH A 40 640 137 HOH HOH . I 3 HOH A 41 641 142 HOH HOH . I 3 HOH A 42 642 145 HOH HOH . I 3 HOH A 43 643 152 HOH HOH . I 3 HOH A 44 644 153 HOH HOH . I 3 HOH A 45 645 154 HOH HOH . I 3 HOH A 46 646 157 HOH HOH . I 3 HOH A 47 647 159 HOH HOH . I 3 HOH A 48 648 171 HOH HOH . I 3 HOH A 49 649 172 HOH HOH . I 3 HOH A 50 650 176 HOH HOH . I 3 HOH A 51 651 186 HOH HOH . I 3 HOH A 52 652 189 HOH HOH . I 3 HOH A 53 653 196 HOH HOH . I 3 HOH A 54 654 199 HOH HOH . I 3 HOH A 55 655 206 HOH HOH . I 3 HOH A 56 656 209 HOH HOH . I 3 HOH A 57 657 216 HOH HOH . I 3 HOH A 58 658 220 HOH HOH . I 3 HOH A 59 659 224 HOH HOH . I 3 HOH A 60 660 234 HOH HOH . I 3 HOH A 61 661 239 HOH HOH . I 3 HOH A 62 662 240 HOH HOH . I 3 HOH A 63 663 254 HOH HOH . J 3 HOH B 1 601 1 HOH HOH . J 3 HOH B 2 602 7 HOH HOH . J 3 HOH B 3 603 10 HOH HOH . J 3 HOH B 4 604 13 HOH HOH . J 3 HOH B 5 605 18 HOH HOH . J 3 HOH B 6 606 25 HOH HOH . J 3 HOH B 7 607 31 HOH HOH . J 3 HOH B 8 608 34 HOH HOH . J 3 HOH B 9 609 36 HOH HOH . J 3 HOH B 10 610 44 HOH HOH . J 3 HOH B 11 611 47 HOH HOH . J 3 HOH B 12 612 54 HOH HOH . J 3 HOH B 13 613 57 HOH HOH . J 3 HOH B 14 614 68 HOH HOH . J 3 HOH B 15 615 71 HOH HOH . J 3 HOH B 16 616 93 HOH HOH . J 3 HOH B 17 617 95 HOH HOH . J 3 HOH B 18 618 97 HOH HOH . J 3 HOH B 19 619 105 HOH HOH . J 3 HOH B 20 620 110 HOH HOH . J 3 HOH B 21 621 112 HOH HOH . J 3 HOH B 22 622 116 HOH HOH . J 3 HOH B 23 623 118 HOH HOH . J 3 HOH B 24 624 124 HOH HOH . J 3 HOH B 25 625 133 HOH HOH . J 3 HOH B 26 626 138 HOH HOH . J 3 HOH B 27 627 139 HOH HOH . J 3 HOH B 28 628 140 HOH HOH . J 3 HOH B 29 629 149 HOH HOH . J 3 HOH B 30 630 151 HOH HOH . J 3 HOH B 31 631 156 HOH HOH . J 3 HOH B 32 632 163 HOH HOH . J 3 HOH B 33 633 179 HOH HOH . J 3 HOH B 34 634 181 HOH HOH . J 3 HOH B 35 635 191 HOH HOH . J 3 HOH B 36 636 193 HOH HOH . J 3 HOH B 37 637 198 HOH HOH . J 3 HOH B 38 638 207 HOH HOH . J 3 HOH B 39 639 208 HOH HOH . J 3 HOH B 40 640 212 HOH HOH . J 3 HOH B 41 641 215 HOH HOH . J 3 HOH B 42 642 231 HOH HOH . J 3 HOH B 43 643 232 HOH HOH . J 3 HOH B 44 644 235 HOH HOH . J 3 HOH B 45 645 237 HOH HOH . J 3 HOH B 46 646 241 HOH HOH . J 3 HOH B 47 647 242 HOH HOH . J 3 HOH B 48 648 245 HOH HOH . J 3 HOH B 49 649 246 HOH HOH . J 3 HOH B 50 650 250 HOH HOH . J 3 HOH B 51 651 253 HOH HOH . K 3 HOH C 1 601 8 HOH HOH . K 3 HOH C 2 602 14 HOH HOH . K 3 HOH C 3 603 27 HOH HOH . K 3 HOH C 4 604 37 HOH HOH . K 3 HOH C 5 605 48 HOH HOH . K 3 HOH C 6 606 58 HOH HOH . K 3 HOH C 7 607 59 HOH HOH . K 3 HOH C 8 608 61 HOH HOH . K 3 HOH C 9 609 62 HOH HOH . K 3 HOH C 10 610 64 HOH HOH . K 3 HOH C 11 611 65 HOH HOH . K 3 HOH C 12 612 66 HOH HOH . K 3 HOH C 13 613 69 HOH HOH . K 3 HOH C 14 614 75 HOH HOH . K 3 HOH C 15 615 80 HOH HOH . K 3 HOH C 16 616 82 HOH HOH . K 3 HOH C 17 617 89 HOH HOH . K 3 HOH C 18 618 99 HOH HOH . K 3 HOH C 19 619 102 HOH HOH . K 3 HOH C 20 620 107 HOH HOH . K 3 HOH C 21 621 108 HOH HOH . K 3 HOH C 22 622 122 HOH HOH . K 3 HOH C 23 623 141 HOH HOH . K 3 HOH C 24 624 144 HOH HOH . K 3 HOH C 25 625 148 HOH HOH . K 3 HOH C 26 626 150 HOH HOH . K 3 HOH C 27 627 160 HOH HOH . K 3 HOH C 28 628 161 HOH HOH . K 3 HOH C 29 629 162 HOH HOH . K 3 HOH C 30 630 164 HOH HOH . K 3 HOH C 31 631 167 HOH HOH . K 3 HOH C 32 632 170 HOH HOH . K 3 HOH C 33 633 177 HOH HOH . K 3 HOH C 34 634 178 HOH HOH . K 3 HOH C 35 635 195 HOH HOH . K 3 HOH C 36 636 200 HOH HOH . K 3 HOH C 37 637 203 HOH HOH . K 3 HOH C 38 638 210 HOH HOH . K 3 HOH C 39 639 217 HOH HOH . K 3 HOH C 40 640 218 HOH HOH . K 3 HOH C 41 641 219 HOH HOH . K 3 HOH C 42 642 222 HOH HOH . K 3 HOH C 43 643 225 HOH HOH . K 3 HOH C 44 644 227 HOH HOH . K 3 HOH C 45 645 228 HOH HOH . K 3 HOH C 46 646 230 HOH HOH . K 3 HOH C 47 647 244 HOH HOH . K 3 HOH C 48 648 249 HOH HOH . K 3 HOH C 49 649 251 HOH HOH . K 3 HOH C 50 650 256 HOH HOH . K 3 HOH C 51 651 257 HOH HOH . L 3 HOH D 1 601 3 HOH HOH . L 3 HOH D 2 602 5 HOH HOH . L 3 HOH D 3 603 9 HOH HOH . L 3 HOH D 4 604 11 HOH HOH . L 3 HOH D 5 605 12 HOH HOH . L 3 HOH D 6 606 17 HOH HOH . L 3 HOH D 7 607 21 HOH HOH . L 3 HOH D 8 608 23 HOH HOH . L 3 HOH D 9 609 24 HOH HOH . L 3 HOH D 10 610 33 HOH HOH . L 3 HOH D 11 611 41 HOH HOH . L 3 HOH D 12 612 42 HOH HOH . L 3 HOH D 13 613 45 HOH HOH . L 3 HOH D 14 614 49 HOH HOH . L 3 HOH D 15 615 50 HOH HOH . L 3 HOH D 16 616 53 HOH HOH . L 3 HOH D 17 617 56 HOH HOH . L 3 HOH D 18 618 74 HOH HOH . L 3 HOH D 19 619 76 HOH HOH . L 3 HOH D 20 620 79 HOH HOH . L 3 HOH D 21 621 81 HOH HOH . L 3 HOH D 22 622 84 HOH HOH . L 3 HOH D 23 623 86 HOH HOH . L 3 HOH D 24 624 88 HOH HOH . L 3 HOH D 25 625 92 HOH HOH . L 3 HOH D 26 626 94 HOH HOH . L 3 HOH D 27 627 96 HOH HOH . L 3 HOH D 28 628 98 HOH HOH . L 3 HOH D 29 629 100 HOH HOH . L 3 HOH D 30 630 101 HOH HOH . L 3 HOH D 31 631 119 HOH HOH . L 3 HOH D 32 632 120 HOH HOH . L 3 HOH D 33 633 121 HOH HOH . L 3 HOH D 34 634 127 HOH HOH . L 3 HOH D 35 635 129 HOH HOH . L 3 HOH D 36 636 134 HOH HOH . L 3 HOH D 37 637 135 HOH HOH . L 3 HOH D 38 638 143 HOH HOH . L 3 HOH D 39 639 146 HOH HOH . L 3 HOH D 40 640 155 HOH HOH . L 3 HOH D 41 641 158 HOH HOH . L 3 HOH D 42 642 166 HOH HOH . L 3 HOH D 43 643 168 HOH HOH . L 3 HOH D 44 644 183 HOH HOH . L 3 HOH D 45 645 185 HOH HOH . L 3 HOH D 46 646 187 HOH HOH . L 3 HOH D 47 647 190 HOH HOH . L 3 HOH D 48 648 194 HOH HOH . L 3 HOH D 49 649 205 HOH HOH . L 3 HOH D 50 650 211 HOH HOH . L 3 HOH D 51 651 221 HOH HOH . L 3 HOH D 52 652 223 HOH HOH . L 3 HOH D 53 653 226 HOH HOH . L 3 HOH D 54 654 229 HOH HOH . L 3 HOH D 55 655 236 HOH HOH . L 3 HOH D 56 656 238 HOH HOH . L 3 HOH D 57 657 247 HOH HOH . L 3 HOH D 58 658 255 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 P PB GDP . . . F 2 56.565 34.598 80.162 1 21.57 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 2 55.292 34.864 80.9 1 18.42 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 2 57.645 35.59 80.519 1 17.42 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 2 56.329 34.491 78.637 1 20.21 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 2 57.29 33.311 80.755 1 19.89 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 2 56.645 31.882 80.687 1 18.03 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 2 55.176 31.882 81.048 1 14.17 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 2 57.695 30.983 81.315 1 19.32 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 2 56.609 31.541 79.094 1 17.31 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 2 57.751 31.003 78.501 1 14.23 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 2 57.188 30.152 77.381 1 21.41 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 2 57.97 30.344 76.18 1 18.39 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 2 57.373 28.707 77.833 1 21.07 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 2 56.531 27.856 77.047 1 20.09 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 2 58.774 28.402 77.388 1 18.35 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 2 58.932 26.978 77.222 1 22.1 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 2 58.74 29.099 76.062 1 15.42 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 2 60.088 29.35 75.59 1 15.46 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 2 61.229 29.614 76.288 1 15.45 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 2 62.257 29.751 75.403 1 14.04 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 2 61.778 29.559 74.148 1 12.73 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 2 62.313 29.619 72.756 1 13.41 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 2 63.512 29.89 72.507 1 15.85 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 2 61.461 29.397 71.766 1 8.92 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 2 60.16 29.147 71.981 1 13.47 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 2 59.401 28.947 70.902 1 14.99 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 2 59.55 29.099 73.201 1 12.05 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 2 60.339 29.301 74.289 1 12.81 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 28 #