data_7Z0F # _model_server_result.job_id ufNDd3SvoAfaP7Y2MVYtkw _model_server_result.datetime_utc '2024-11-26 05:53:12' _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 7z0f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":600}' # _entry.id 7Z0F # _exptl.entry_id 7Z0F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.61 _cell.angle_gamma 90 _cell.entry_id 7Z0F _cell.length_a 54.28 _cell.length_b 86.71 _cell.length_c 137.61 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z0F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 E O2G GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc2 E O1B GTP . A GTP 600 1_555 F MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc3 F MG MG . A MG 601 1_555 I O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc4 F MG MG . A MG 601 1_555 I O HOH . A HOH 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc5 F MG MG . A MG 601 1_555 I O HOH . A HOH 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc6 F MG MG . A MG 601 1_555 I O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? # _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 7Z0F _atom_sites.fract_transf_matrix[1][1] 0.018423 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002135 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011533 _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] 0.007316 _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 5 GTP A 1 600 600 GTP GTP . F 6 MG A 1 601 601 MG MG . G 7 GDP B 1 600 600 GDP GDP . H 8 GOL C 1 500 500 GOL GOL . I 9 HOH A 1 701 143 HOH HOH . I 9 HOH A 2 702 107 HOH HOH . I 9 HOH A 3 703 602 HOH HOH . I 9 HOH A 4 704 13 HOH HOH . I 9 HOH A 5 705 79 HOH HOH . I 9 HOH A 6 706 19 HOH HOH . I 9 HOH A 7 707 145 HOH HOH . I 9 HOH A 8 708 66 HOH HOH . I 9 HOH A 9 709 51 HOH HOH . I 9 HOH A 10 710 59 HOH HOH . I 9 HOH A 11 711 80 HOH HOH . I 9 HOH A 12 712 121 HOH HOH . I 9 HOH A 13 713 604 HOH HOH . I 9 HOH A 14 714 92 HOH HOH . I 9 HOH A 15 715 14 HOH HOH . I 9 HOH A 16 716 603 HOH HOH . I 9 HOH A 17 717 1 HOH HOH . I 9 HOH A 18 718 128 HOH HOH . I 9 HOH A 19 719 2 HOH HOH . I 9 HOH A 20 720 81 HOH HOH . I 9 HOH A 21 721 605 HOH HOH . I 9 HOH A 22 722 106 HOH HOH . I 9 HOH A 23 723 17 HOH HOH . I 9 HOH A 24 724 43 HOH HOH . I 9 HOH A 25 725 83 HOH HOH . I 9 HOH A 26 726 88 HOH HOH . I 9 HOH A 27 727 18 HOH HOH . I 9 HOH A 28 728 30 HOH HOH . I 9 HOH A 29 729 103 HOH HOH . I 9 HOH A 30 730 87 HOH HOH . I 9 HOH A 31 731 38 HOH HOH . I 9 HOH A 32 732 151 HOH HOH . I 9 HOH A 33 733 16 HOH HOH . I 9 HOH A 34 734 86 HOH HOH . I 9 HOH A 35 735 54 HOH HOH . I 9 HOH A 36 736 91 HOH HOH . I 9 HOH A 37 737 85 HOH HOH . I 9 HOH A 38 738 144 HOH HOH . I 9 HOH A 39 739 77 HOH HOH . I 9 HOH A 40 740 117 HOH HOH . I 9 HOH A 41 741 4 HOH HOH . I 9 HOH A 42 742 31 HOH HOH . I 9 HOH A 43 743 37 HOH HOH . I 9 HOH A 44 744 12 HOH HOH . I 9 HOH A 45 745 95 HOH HOH . I 9 HOH A 46 746 41 HOH HOH . I 9 HOH A 47 747 135 HOH HOH . I 9 HOH A 48 748 125 HOH HOH . I 9 HOH A 49 749 25 HOH HOH . I 9 HOH A 50 750 137 HOH HOH . I 9 HOH A 51 751 55 HOH HOH . I 9 HOH A 52 752 46 HOH HOH . I 9 HOH A 53 753 29 HOH HOH . I 9 HOH A 54 754 8 HOH HOH . I 9 HOH A 55 755 39 HOH HOH . I 9 HOH A 56 756 5 HOH HOH . I 9 HOH A 57 757 120 HOH HOH . I 9 HOH A 58 758 28 HOH HOH . I 9 HOH A 59 759 24 HOH HOH . I 9 HOH A 60 760 67 HOH HOH . I 9 HOH A 61 761 148 HOH HOH . I 9 HOH A 62 762 23 HOH HOH . I 9 HOH A 63 763 32 HOH HOH . I 9 HOH A 64 764 147 HOH HOH . I 9 HOH A 65 765 138 HOH HOH . I 9 HOH A 66 766 132 HOH HOH . I 9 HOH A 67 767 113 HOH HOH . I 9 HOH A 68 768 26 HOH HOH . I 9 HOH A 69 769 11 HOH HOH . I 9 HOH A 70 770 9 HOH HOH . I 9 HOH A 71 771 6 HOH HOH . I 9 HOH A 72 772 15 HOH HOH . I 9 HOH A 73 773 108 HOH HOH . I 9 HOH A 74 774 105 HOH HOH . I 9 HOH A 75 775 61 HOH HOH . I 9 HOH A 76 776 33 HOH HOH . I 9 HOH A 77 777 94 HOH HOH . I 9 HOH A 78 778 69 HOH HOH . I 9 HOH A 79 779 74 HOH HOH . I 9 HOH A 80 780 127 HOH HOH . I 9 HOH A 81 781 56 HOH HOH . I 9 HOH A 82 782 20 HOH HOH . I 9 HOH A 83 783 136 HOH HOH . I 9 HOH A 84 784 21 HOH HOH . I 9 HOH A 85 785 90 HOH HOH . I 9 HOH A 86 786 64 HOH HOH . I 9 HOH A 87 787 142 HOH HOH . I 9 HOH A 88 788 118 HOH HOH . I 9 HOH A 89 789 82 HOH HOH . I 9 HOH A 90 790 34 HOH HOH . I 9 HOH A 91 791 129 HOH HOH . I 9 HOH A 92 792 114 HOH HOH . I 9 HOH A 93 793 40 HOH HOH . I 9 HOH A 94 794 45 HOH HOH . I 9 HOH A 95 795 48 HOH HOH . I 9 HOH A 96 796 116 HOH HOH . I 9 HOH A 97 797 65 HOH HOH . I 9 HOH A 98 798 98 HOH HOH . I 9 HOH A 99 799 62 HOH HOH . I 9 HOH A 100 800 27 HOH HOH . I 9 HOH A 101 801 50 HOH HOH . I 9 HOH A 102 802 93 HOH HOH . I 9 HOH A 103 803 22 HOH HOH . I 9 HOH A 104 804 71 HOH HOH . I 9 HOH A 105 805 49 HOH HOH . I 9 HOH A 106 806 140 HOH HOH . I 9 HOH A 107 807 149 HOH HOH . I 9 HOH A 108 808 101 HOH HOH . I 9 HOH A 109 809 124 HOH HOH . I 9 HOH A 110 810 60 HOH HOH . I 9 HOH A 111 811 139 HOH HOH . I 9 HOH A 112 812 109 HOH HOH . I 9 HOH A 113 813 131 HOH HOH . I 9 HOH A 114 814 123 HOH HOH . J 9 HOH C 1 601 99 HOH HOH . J 9 HOH C 2 602 150 HOH HOH . J 9 HOH C 3 603 153 HOH HOH . J 9 HOH C 4 604 146 HOH HOH . J 9 HOH C 5 605 141 HOH HOH . J 9 HOH C 6 606 44 HOH HOH . J 9 HOH C 7 607 47 HOH HOH . J 9 HOH C 8 608 3 HOH HOH . J 9 HOH C 9 609 133 HOH HOH . J 9 HOH C 10 610 110 HOH HOH . J 9 HOH C 11 611 119 HOH HOH . J 9 HOH C 12 612 70 HOH HOH . J 9 HOH C 13 613 111 HOH HOH . J 9 HOH C 14 614 57 HOH HOH . J 9 HOH C 15 615 7 HOH HOH . J 9 HOH C 16 616 97 HOH HOH . J 9 HOH C 17 617 10 HOH HOH . J 9 HOH C 18 618 122 HOH HOH . J 9 HOH C 19 619 89 HOH HOH . J 9 HOH C 20 620 102 HOH HOH . J 9 HOH C 21 621 42 HOH HOH . J 9 HOH C 22 622 63 HOH HOH . J 9 HOH C 23 623 84 HOH HOH . J 9 HOH C 24 624 73 HOH HOH . J 9 HOH C 25 625 68 HOH HOH . J 9 HOH C 26 626 155 HOH HOH . J 9 HOH C 27 627 115 HOH HOH . J 9 HOH C 28 628 52 HOH HOH . J 9 HOH C 29 629 72 HOH HOH . J 9 HOH C 30 630 134 HOH HOH . J 9 HOH C 31 631 96 HOH HOH . J 9 HOH C 32 632 130 HOH HOH . J 9 HOH C 33 633 75 HOH HOH . J 9 HOH C 34 634 36 HOH HOH . J 9 HOH C 35 635 154 HOH HOH . J 9 HOH C 36 636 104 HOH HOH . J 9 HOH C 37 637 58 HOH HOH . J 9 HOH C 38 638 35 HOH HOH . J 9 HOH C 39 639 78 HOH HOH . J 9 HOH C 40 640 152 HOH HOH . J 9 HOH C 41 641 112 HOH HOH . J 9 HOH C 42 642 100 HOH HOH . J 9 HOH C 43 643 76 HOH HOH . J 9 HOH C 44 644 53 HOH HOH . K 9 HOH P 1 401 126 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 . . . G 7 -4.492 16.423 -67.6 1 158.43 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . G 7 -3.907 15.614 -68.767 1 158.63 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . G 7 -4.695 15.5 -66.411 1 158.31 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . G 7 -3.646 17.618 -67.291 1 158.49 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . G 7 -5.966 16.846 -68.034 1 158.26 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . G 7 -7.163 17.535 -67.24 1 158.02 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . G 7 -7.447 18.886 -67.92 1 157.97 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . G 7 -6.733 17.771 -65.844 1 158.14 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . G 7 -8.48 16.592 -67.313 1 157.64 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . G 7 -9.701 16.944 -67.998 1 157.39 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . G 7 -10.853 16.828 -67.03 1 157.23 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . G 7 -10.631 17.703 -65.903 1 157.36 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . G 7 -12.231 17.192 -67.581 1 156.96 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . G 7 -13.228 16.333 -67.039 1 156.68 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . G 7 -12.389 18.657 -67.16 1 157.03 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . G 7 -13.749 19.057 -67.028 1 156.79 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . G 7 -11.67 18.66 -65.81 1 157.35 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . G 7 -11.07 19.957 -65.452 1 157.52 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . G 7 -10.077 20.625 -66.122 1 157.55 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . G 7 -9.694 21.729 -65.527 1 157.54 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . G 7 -10.489 21.796 -64.393 1 157.52 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . G 7 -10.541 22.761 -63.33 1 157.48 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . G 7 -9.844 23.767 -63.198 1 157.45 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . G 7 -11.499 22.442 -62.387 1 157.48 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . G 7 -12.318 21.345 -62.432 1 157.45 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . G 7 -13.217 21.223 -61.453 1 157.3 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . G 7 -12.273 20.434 -63.401 1 157.5 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . G 7 -11.348 20.715 -64.339 1 157.5 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 41 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #