data_5VGR # _model_server_result.job_id 1FNeomZdSlFFxfEWpT6hsw _model_server_result.datetime_utc '2025-03-31 13:14:01' _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 5vgr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5VGR # _exptl.entry_id 5VGR _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.22 _cell.angle_gamma 90 _cell.entry_id 5VGR _cell.length_a 130.666 _cell.length_b 57.057 _cell.length_c 143.423 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VGR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 D 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 5VGR _atom_sites.fract_transf_matrix[1][1] 0.007653 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003769 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017526 _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] 0.007772 _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 GDP A 1 501 1 GDP GDP . D 2 GDP B 1 501 2 GDP GDP . E 3 HOH A 1 601 181 HOH HOH . E 3 HOH A 2 602 156 HOH HOH . E 3 HOH A 3 603 124 HOH HOH . E 3 HOH A 4 604 72 HOH HOH . E 3 HOH A 5 605 144 HOH HOH . E 3 HOH A 6 606 132 HOH HOH . E 3 HOH A 7 607 48 HOH HOH . E 3 HOH A 8 608 239 HOH HOH . E 3 HOH A 9 609 237 HOH HOH . E 3 HOH A 10 610 228 HOH HOH . E 3 HOH A 11 611 35 HOH HOH . E 3 HOH A 12 612 41 HOH HOH . E 3 HOH A 13 613 186 HOH HOH . E 3 HOH A 14 614 206 HOH HOH . E 3 HOH A 15 615 195 HOH HOH . E 3 HOH A 16 616 53 HOH HOH . E 3 HOH A 17 617 166 HOH HOH . E 3 HOH A 18 618 42 HOH HOH . E 3 HOH A 19 619 85 HOH HOH . E 3 HOH A 20 620 60 HOH HOH . E 3 HOH A 21 621 68 HOH HOH . E 3 HOH A 22 622 36 HOH HOH . E 3 HOH A 23 623 89 HOH HOH . E 3 HOH A 24 624 15 HOH HOH . E 3 HOH A 25 625 127 HOH HOH . E 3 HOH A 26 626 8 HOH HOH . E 3 HOH A 27 627 81 HOH HOH . E 3 HOH A 28 628 69 HOH HOH . E 3 HOH A 29 629 103 HOH HOH . E 3 HOH A 30 630 28 HOH HOH . E 3 HOH A 31 631 1 HOH HOH . E 3 HOH A 32 632 39 HOH HOH . E 3 HOH A 33 633 66 HOH HOH . E 3 HOH A 34 634 82 HOH HOH . E 3 HOH A 35 635 114 HOH HOH . E 3 HOH A 36 636 2 HOH HOH . E 3 HOH A 37 637 88 HOH HOH . E 3 HOH A 38 638 189 HOH HOH . E 3 HOH A 39 639 142 HOH HOH . E 3 HOH A 40 640 241 HOH HOH . E 3 HOH A 41 641 55 HOH HOH . E 3 HOH A 42 642 160 HOH HOH . E 3 HOH A 43 643 6 HOH HOH . E 3 HOH A 44 644 13 HOH HOH . E 3 HOH A 45 645 26 HOH HOH . E 3 HOH A 46 646 111 HOH HOH . E 3 HOH A 47 647 58 HOH HOH . E 3 HOH A 48 648 113 HOH HOH . E 3 HOH A 49 649 57 HOH HOH . E 3 HOH A 50 650 187 HOH HOH . E 3 HOH A 51 651 97 HOH HOH . E 3 HOH A 52 652 123 HOH HOH . E 3 HOH A 53 653 20 HOH HOH . E 3 HOH A 54 654 84 HOH HOH . E 3 HOH A 55 655 52 HOH HOH . E 3 HOH A 56 656 43 HOH HOH . E 3 HOH A 57 657 14 HOH HOH . E 3 HOH A 58 658 152 HOH HOH . E 3 HOH A 59 659 46 HOH HOH . E 3 HOH A 60 660 74 HOH HOH . E 3 HOH A 61 661 37 HOH HOH . E 3 HOH A 62 662 161 HOH HOH . E 3 HOH A 63 663 125 HOH HOH . E 3 HOH A 64 664 67 HOH HOH . E 3 HOH A 65 665 38 HOH HOH . E 3 HOH A 66 666 109 HOH HOH . E 3 HOH A 67 667 147 HOH HOH . E 3 HOH A 68 668 23 HOH HOH . E 3 HOH A 69 669 65 HOH HOH . E 3 HOH A 70 670 90 HOH HOH . E 3 HOH A 71 671 148 HOH HOH . E 3 HOH A 72 672 201 HOH HOH . E 3 HOH A 73 673 19 HOH HOH . E 3 HOH A 74 674 27 HOH HOH . E 3 HOH A 75 675 64 HOH HOH . E 3 HOH A 76 676 22 HOH HOH . E 3 HOH A 77 677 10 HOH HOH . E 3 HOH A 78 678 93 HOH HOH . E 3 HOH A 79 679 51 HOH HOH . E 3 HOH A 80 680 54 HOH HOH . E 3 HOH A 81 681 33 HOH HOH . E 3 HOH A 82 682 70 HOH HOH . E 3 HOH A 83 683 9 HOH HOH . E 3 HOH A 84 684 98 HOH HOH . E 3 HOH A 85 685 139 HOH HOH . E 3 HOH A 86 686 224 HOH HOH . E 3 HOH A 87 687 145 HOH HOH . E 3 HOH A 88 688 118 HOH HOH . E 3 HOH A 89 689 193 HOH HOH . E 3 HOH A 90 690 21 HOH HOH . E 3 HOH A 91 691 157 HOH HOH . E 3 HOH A 92 692 104 HOH HOH . E 3 HOH A 93 693 153 HOH HOH . E 3 HOH A 94 694 200 HOH HOH . E 3 HOH A 95 695 79 HOH HOH . E 3 HOH A 96 696 203 HOH HOH . E 3 HOH A 97 697 61 HOH HOH . E 3 HOH A 98 698 25 HOH HOH . E 3 HOH A 99 699 242 HOH HOH . E 3 HOH A 100 700 11 HOH HOH . E 3 HOH A 101 701 159 HOH HOH . E 3 HOH A 102 702 168 HOH HOH . E 3 HOH A 103 703 96 HOH HOH . E 3 HOH A 104 704 236 HOH HOH . E 3 HOH A 105 705 172 HOH HOH . E 3 HOH A 106 706 94 HOH HOH . E 3 HOH A 107 707 169 HOH HOH . E 3 HOH A 108 708 112 HOH HOH . E 3 HOH A 109 709 211 HOH HOH . E 3 HOH A 110 710 30 HOH HOH . E 3 HOH A 111 711 138 HOH HOH . E 3 HOH A 112 712 234 HOH HOH . E 3 HOH A 113 713 108 HOH HOH . E 3 HOH A 114 714 158 HOH HOH . E 3 HOH A 115 715 5 HOH HOH . E 3 HOH A 116 716 45 HOH HOH . E 3 HOH A 117 717 216 HOH HOH . E 3 HOH A 118 718 3 HOH HOH . E 3 HOH A 119 719 12 HOH HOH . E 3 HOH A 120 720 18 HOH HOH . E 3 HOH A 121 721 227 HOH HOH . E 3 HOH A 122 722 106 HOH HOH . E 3 HOH A 123 723 47 HOH HOH . E 3 HOH A 124 724 120 HOH HOH . E 3 HOH A 125 725 83 HOH HOH . E 3 HOH A 126 726 238 HOH HOH . E 3 HOH A 127 727 34 HOH HOH . E 3 HOH A 128 728 95 HOH HOH . E 3 HOH A 129 729 137 HOH HOH . E 3 HOH A 130 730 76 HOH HOH . E 3 HOH A 131 731 44 HOH HOH . E 3 HOH A 132 732 121 HOH HOH . E 3 HOH A 133 733 177 HOH HOH . E 3 HOH A 134 734 149 HOH HOH . E 3 HOH A 135 735 146 HOH HOH . E 3 HOH A 136 736 209 HOH HOH . E 3 HOH A 137 737 91 HOH HOH . E 3 HOH A 138 738 180 HOH HOH . E 3 HOH A 139 739 204 HOH HOH . E 3 HOH A 140 740 188 HOH HOH . E 3 HOH A 141 741 162 HOH HOH . E 3 HOH A 142 742 184 HOH HOH . E 3 HOH A 143 743 101 HOH HOH . E 3 HOH A 144 744 31 HOH HOH . E 3 HOH A 145 745 50 HOH HOH . E 3 HOH A 146 746 119 HOH HOH . E 3 HOH A 147 747 233 HOH HOH . E 3 HOH A 148 748 226 HOH HOH . E 3 HOH A 149 749 175 HOH HOH . E 3 HOH A 150 750 179 HOH HOH . E 3 HOH A 151 751 32 HOH HOH . E 3 HOH A 152 752 77 HOH HOH . E 3 HOH A 153 753 141 HOH HOH . E 3 HOH A 154 754 229 HOH HOH . E 3 HOH A 155 755 136 HOH HOH . E 3 HOH A 156 756 176 HOH HOH . E 3 HOH A 157 757 128 HOH HOH . E 3 HOH A 158 758 92 HOH HOH . E 3 HOH A 159 759 222 HOH HOH . E 3 HOH A 160 760 185 HOH HOH . E 3 HOH A 161 761 215 HOH HOH . E 3 HOH A 162 762 199 HOH HOH . E 3 HOH A 163 763 219 HOH HOH . E 3 HOH A 164 764 220 HOH HOH . E 3 HOH A 165 765 105 HOH HOH . E 3 HOH A 166 766 130 HOH HOH . E 3 HOH A 167 767 225 HOH HOH . E 3 HOH A 168 768 208 HOH HOH . E 3 HOH A 169 769 196 HOH HOH . E 3 HOH A 170 770 110 HOH HOH . E 3 HOH A 171 771 174 HOH HOH . E 3 HOH A 172 772 210 HOH HOH . E 3 HOH A 173 773 116 HOH HOH . E 3 HOH A 174 774 197 HOH HOH . E 3 HOH A 175 775 205 HOH HOH . E 3 HOH A 176 776 198 HOH HOH . E 3 HOH A 177 777 171 HOH HOH . E 3 HOH A 178 778 150 HOH HOH . E 3 HOH A 179 779 178 HOH HOH . E 3 HOH A 180 780 134 HOH HOH . E 3 HOH A 181 781 122 HOH HOH . E 3 HOH A 182 782 235 HOH HOH . E 3 HOH A 183 783 155 HOH HOH . E 3 HOH A 184 784 140 HOH HOH . E 3 HOH A 185 785 173 HOH HOH . F 3 HOH B 1 601 212 HOH HOH . F 3 HOH B 2 602 240 HOH HOH . F 3 HOH B 3 603 135 HOH HOH . F 3 HOH B 4 604 7 HOH HOH . F 3 HOH B 5 605 49 HOH HOH . F 3 HOH B 6 606 17 HOH HOH . F 3 HOH B 7 607 133 HOH HOH . F 3 HOH B 8 608 4 HOH HOH . F 3 HOH B 9 609 63 HOH HOH . F 3 HOH B 10 610 115 HOH HOH . F 3 HOH B 11 611 221 HOH HOH . F 3 HOH B 12 612 191 HOH HOH . F 3 HOH B 13 613 223 HOH HOH . F 3 HOH B 14 614 62 HOH HOH . F 3 HOH B 15 615 218 HOH HOH . F 3 HOH B 16 616 231 HOH HOH . F 3 HOH B 17 617 80 HOH HOH . F 3 HOH B 18 618 183 HOH HOH . F 3 HOH B 19 619 99 HOH HOH . F 3 HOH B 20 620 131 HOH HOH . F 3 HOH B 21 621 102 HOH HOH . F 3 HOH B 22 622 40 HOH HOH . F 3 HOH B 23 623 170 HOH HOH . F 3 HOH B 24 624 24 HOH HOH . F 3 HOH B 25 625 207 HOH HOH . F 3 HOH B 26 626 143 HOH HOH . F 3 HOH B 27 627 29 HOH HOH . F 3 HOH B 28 628 213 HOH HOH . F 3 HOH B 29 629 194 HOH HOH . F 3 HOH B 30 630 163 HOH HOH . F 3 HOH B 31 631 167 HOH HOH . F 3 HOH B 32 632 71 HOH HOH . F 3 HOH B 33 633 16 HOH HOH . F 3 HOH B 34 634 86 HOH HOH . F 3 HOH B 35 635 243 HOH HOH . F 3 HOH B 36 636 100 HOH HOH . F 3 HOH B 37 637 126 HOH HOH . F 3 HOH B 38 638 165 HOH HOH . F 3 HOH B 39 639 192 HOH HOH . F 3 HOH B 40 640 214 HOH HOH . F 3 HOH B 41 641 75 HOH HOH . F 3 HOH B 42 642 232 HOH HOH . F 3 HOH B 43 643 87 HOH HOH . F 3 HOH B 44 644 73 HOH HOH . F 3 HOH B 45 645 78 HOH HOH . F 3 HOH B 46 646 59 HOH HOH . F 3 HOH B 47 647 107 HOH HOH . F 3 HOH B 48 648 129 HOH HOH . F 3 HOH B 49 649 202 HOH HOH . F 3 HOH B 50 650 190 HOH HOH . F 3 HOH B 51 651 117 HOH HOH . F 3 HOH B 52 652 164 HOH HOH . F 3 HOH B 53 653 230 HOH HOH . F 3 HOH B 54 654 182 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 . . . C 2 132.016 3.02 29.313 1 35 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . C 2 131.003 3.798 28.511 1 33.21 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . C 2 133.288 2.789 28.529 1 36.66 -1 O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . C 2 132.267 3.83 30.576 1 43.09 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . C 2 131.342 1.638 29.753 1 39.33 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . C 2 132.02 0.192 29.772 1 37.95 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . C 2 132.346 -0.293 28.389 1 38.98 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . C 2 133.182 0.15 30.728 1 44.85 -1 O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . C 2 130.793 -0.708 30.319 1 44.91 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . C 2 130.149 -0.478 31.569 1 42.46 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . C 2 129.416 -1.748 31.998 1 45.79 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . C 2 128.401 -2.096 31.05 1 34.93 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . C 2 130.348 -2.945 32.055 1 42.16 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . C 2 129.835 -3.787 33.089 1 46.49 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . C 2 130.15 -3.62 30.713 1 31.91 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . C 2 130.493 -5.012 30.717 1 38.38 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . C 2 128.667 -3.384 30.482 1 28.21 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . C 2 128.314 -3.29 29.055 1 40.05 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . C 2 129.126 -3.138 27.976 1 32.15 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . C 2 128.368 -3.06 26.841 1 40.33 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . C 2 127.069 -3.151 27.202 1 35.88 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . C 2 125.752 -3.151 26.534 1 34.15 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . C 2 125.664 -3.033 25.289 1 31.37 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . C 2 124.656 -3.28 27.3 1 30.81 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . C 2 124.711 -3.401 28.647 1 41.71 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . C 2 123.567 -3.531 29.378 1 39.65 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . C 2 125.879 -3.412 29.321 1 32.89 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . C 2 127.05 -3.288 28.663 1 38.18 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #