data_5GYZ # _model_server_result.job_id N4-EreS0rhGAluP30dVJOg _model_server_result.datetime_utc '2024-10-20 03:32:25' _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 5gyz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5GYZ # _exptl.entry_id 5GYZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 90 _cell.angle_gamma 90 _cell.entry_id 5GYZ _cell.length_a 73.443 _cell.length_b 73.443 _cell.length_c 96.07 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GYZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id OXT _struct_conn.ptnr1_label_comp_id 7BV _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id 7BV _struct_conn.ptnr1_auth_seq_id 500 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id P _struct_conn.ptnr2_label_comp_id AMP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id AMP _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 1.45 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _chem_comp.type non-polymer _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 P O1P AMP doub 59 n n P O2P AMP sing 60 n n P O3P AMP sing 61 n n P O5' AMP sing 62 n n O2P HOP2 AMP sing 63 n n O3P HOP3 AMP sing 64 n n O5' C5' AMP sing 65 n n C5' C4' AMP sing 66 n n C5' "H5'1" AMP sing 67 n n C5' "H5'2" AMP sing 68 n n C4' O4' AMP sing 69 n n C4' C3' AMP sing 70 n n C4' H4' AMP sing 71 n n O4' C1' AMP sing 72 n n C3' O3' AMP sing 73 n n C3' C2' AMP sing 74 n n C3' H3' AMP sing 75 n n O3' HO3' AMP sing 76 n n C2' O2' AMP sing 77 n n C2' C1' AMP sing 78 n n C2' H2' AMP sing 79 n n O2' HO2' AMP sing 80 n n C1' N9 AMP sing 81 n n C1' H1' AMP sing 82 n n N9 C8 AMP sing 83 n y N9 C4 AMP sing 84 n y C8 N7 AMP doub 85 n y C8 H8 AMP sing 86 n n N7 C5 AMP sing 87 n y C5 C6 AMP sing 88 n y C5 C4 AMP doub 89 n y C6 N6 AMP sing 90 n n C6 N1 AMP doub 91 n y N6 HN61 AMP sing 92 n n N6 HN62 AMP sing 93 n n N1 C2 AMP sing 94 n y C2 N3 AMP doub 95 n y C2 H2 AMP sing 96 n n N3 C4 AMP sing 97 n y # _atom_sites.entry_id 5GYZ _atom_sites.fract_transf_matrix[1][1] 0.013616 _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] 0.013616 _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] 0.010409 _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 B 2 7BV A 1 500 500 7BV 7BV . C 3 AMP A 1 501 501 AMP AMP . D 4 PEG A 1 502 502 PEG PEG . E 5 GOL A 1 503 503 GOL GOL . F 5 GOL A 1 504 504 GOL GOL . G 5 GOL A 1 505 505 GOL GOL . H 6 HOH A 1 601 601 HOH HOH . H 6 HOH A 2 602 602 HOH HOH . H 6 HOH A 3 603 603 HOH HOH . H 6 HOH A 4 604 604 HOH HOH . H 6 HOH A 5 605 605 HOH HOH . H 6 HOH A 6 606 606 HOH HOH . H 6 HOH A 7 607 607 HOH HOH . H 6 HOH A 8 608 608 HOH HOH . H 6 HOH A 9 609 609 HOH HOH . H 6 HOH A 10 610 610 HOH HOH . H 6 HOH A 11 611 611 HOH HOH . H 6 HOH A 12 612 612 HOH HOH . H 6 HOH A 13 613 613 HOH HOH . H 6 HOH A 14 614 614 HOH HOH . H 6 HOH A 15 615 615 HOH HOH . H 6 HOH A 16 616 616 HOH HOH . H 6 HOH A 17 617 617 HOH HOH . H 6 HOH A 18 618 618 HOH HOH . H 6 HOH A 19 619 619 HOH HOH . H 6 HOH A 20 620 620 HOH HOH . H 6 HOH A 21 621 621 HOH HOH . H 6 HOH A 22 622 622 HOH HOH . H 6 HOH A 23 623 623 HOH HOH . H 6 HOH A 24 624 624 HOH HOH . H 6 HOH A 25 625 625 HOH HOH . H 6 HOH A 26 626 626 HOH HOH . H 6 HOH A 27 627 627 HOH HOH . H 6 HOH A 28 628 628 HOH HOH . H 6 HOH A 29 629 629 HOH HOH . H 6 HOH A 30 630 630 HOH HOH . H 6 HOH A 31 631 631 HOH HOH . H 6 HOH A 32 632 632 HOH HOH . H 6 HOH A 33 633 633 HOH HOH . H 6 HOH A 34 634 634 HOH HOH . H 6 HOH A 35 635 635 HOH HOH . H 6 HOH A 36 636 636 HOH HOH . H 6 HOH A 37 637 637 HOH HOH . H 6 HOH A 38 638 638 HOH HOH . H 6 HOH A 39 639 639 HOH HOH . H 6 HOH A 40 640 640 HOH HOH . H 6 HOH A 41 641 642 HOH HOH . H 6 HOH A 42 642 643 HOH HOH . H 6 HOH A 43 643 644 HOH HOH . H 6 HOH A 44 644 645 HOH HOH . H 6 HOH A 45 645 646 HOH HOH . H 6 HOH A 46 646 647 HOH HOH . H 6 HOH A 47 647 648 HOH HOH . H 6 HOH A 48 648 649 HOH HOH . H 6 HOH A 49 649 650 HOH HOH . H 6 HOH A 50 650 651 HOH HOH . H 6 HOH A 51 651 652 HOH HOH . H 6 HOH A 52 652 653 HOH HOH . H 6 HOH A 53 653 654 HOH HOH . H 6 HOH A 54 654 655 HOH HOH . H 6 HOH A 55 655 656 HOH HOH . H 6 HOH A 56 656 657 HOH HOH . H 6 HOH A 57 657 658 HOH HOH . H 6 HOH A 58 658 659 HOH HOH . H 6 HOH A 59 659 660 HOH HOH . H 6 HOH A 60 660 661 HOH HOH . H 6 HOH A 61 661 662 HOH HOH . H 6 HOH A 62 662 663 HOH HOH . H 6 HOH A 63 663 664 HOH HOH . H 6 HOH A 64 664 665 HOH HOH . H 6 HOH A 65 665 666 HOH HOH . H 6 HOH A 66 666 667 HOH HOH . H 6 HOH A 67 667 668 HOH HOH . H 6 HOH A 68 668 669 HOH HOH . H 6 HOH A 69 669 670 HOH HOH . H 6 HOH A 70 670 671 HOH HOH . H 6 HOH A 71 671 672 HOH HOH . H 6 HOH A 72 672 673 HOH HOH . H 6 HOH A 73 673 674 HOH HOH . H 6 HOH A 74 674 675 HOH HOH . H 6 HOH A 75 675 641 HOH HOH . H 6 HOH A 76 676 676 HOH HOH . H 6 HOH A 77 677 677 HOH HOH . H 6 HOH A 78 678 678 HOH HOH . H 6 HOH A 79 679 679 HOH HOH . H 6 HOH A 80 680 680 HOH HOH . H 6 HOH A 81 681 681 HOH HOH . H 6 HOH A 82 682 683 HOH HOH . H 6 HOH A 83 683 684 HOH HOH . H 6 HOH A 84 684 685 HOH HOH . H 6 HOH A 85 685 686 HOH HOH . H 6 HOH A 86 686 687 HOH HOH . H 6 HOH A 87 687 688 HOH HOH . H 6 HOH A 88 688 689 HOH HOH . H 6 HOH A 89 689 690 HOH HOH . H 6 HOH A 90 690 691 HOH HOH . H 6 HOH A 91 691 692 HOH HOH . H 6 HOH A 92 692 693 HOH HOH . H 6 HOH A 93 693 694 HOH HOH . H 6 HOH A 94 694 695 HOH HOH . H 6 HOH A 95 695 696 HOH HOH . H 6 HOH A 96 696 697 HOH HOH . H 6 HOH A 97 697 698 HOH HOH . H 6 HOH A 98 698 699 HOH HOH . H 6 HOH A 99 699 700 HOH HOH . H 6 HOH A 100 700 701 HOH HOH . H 6 HOH A 101 701 702 HOH HOH . H 6 HOH A 102 702 703 HOH HOH . H 6 HOH A 103 703 704 HOH HOH . H 6 HOH A 104 704 705 HOH HOH . H 6 HOH A 105 705 706 HOH HOH . H 6 HOH A 106 706 707 HOH HOH . H 6 HOH A 107 707 708 HOH HOH . H 6 HOH A 108 708 709 HOH HOH . H 6 HOH A 109 709 710 HOH HOH . H 6 HOH A 110 710 711 HOH HOH . H 6 HOH A 111 711 712 HOH HOH . H 6 HOH A 112 712 713 HOH HOH . H 6 HOH A 113 713 714 HOH HOH . H 6 HOH A 114 714 715 HOH HOH . H 6 HOH A 115 715 716 HOH HOH . H 6 HOH A 116 716 717 HOH HOH . H 6 HOH A 117 717 718 HOH HOH . H 6 HOH A 118 718 719 HOH HOH . H 6 HOH A 119 719 720 HOH HOH . H 6 HOH A 120 720 721 HOH HOH . H 6 HOH A 121 721 722 HOH HOH . H 6 HOH A 122 722 723 HOH HOH . H 6 HOH A 123 723 724 HOH HOH . H 6 HOH A 124 724 725 HOH HOH . H 6 HOH A 125 725 726 HOH HOH . H 6 HOH A 126 726 727 HOH HOH . H 6 HOH A 127 727 750 HOH HOH . H 6 HOH A 128 728 728 HOH HOH . H 6 HOH A 129 729 730 HOH HOH . H 6 HOH A 130 730 729 HOH HOH . H 6 HOH A 131 731 731 HOH HOH . H 6 HOH A 132 732 732 HOH HOH . H 6 HOH A 133 733 733 HOH HOH . H 6 HOH A 134 734 734 HOH HOH . H 6 HOH A 135 735 735 HOH HOH . H 6 HOH A 136 736 736 HOH HOH . H 6 HOH A 137 737 737 HOH HOH . H 6 HOH A 138 738 738 HOH HOH . H 6 HOH A 139 739 739 HOH HOH . H 6 HOH A 140 740 740 HOH HOH . H 6 HOH A 141 741 682 HOH HOH . H 6 HOH A 142 742 741 HOH HOH . H 6 HOH A 143 743 742 HOH HOH . H 6 HOH A 144 744 743 HOH HOH . H 6 HOH A 145 745 744 HOH HOH . H 6 HOH A 146 746 745 HOH HOH . H 6 HOH A 147 747 746 HOH HOH . H 6 HOH A 148 748 747 HOH HOH . H 6 HOH A 149 749 748 HOH HOH . H 6 HOH A 150 750 749 HOH HOH . H 6 HOH A 151 751 751 HOH HOH . H 6 HOH A 152 752 752 HOH HOH . H 6 HOH A 153 753 753 HOH HOH . H 6 HOH A 154 754 754 HOH HOH . H 6 HOH A 155 755 755 HOH HOH . H 6 HOH A 156 756 756 HOH HOH . H 6 HOH A 157 757 757 HOH HOH . H 6 HOH A 158 758 758 HOH HOH . H 6 HOH A 159 759 759 HOH HOH . H 6 HOH A 160 760 760 HOH HOH . H 6 HOH A 161 761 761 HOH HOH . H 6 HOH A 162 762 762 HOH HOH . H 6 HOH A 163 763 763 HOH HOH . H 6 HOH A 164 764 764 HOH HOH . H 6 HOH A 165 765 765 HOH HOH . H 6 HOH A 166 766 766 HOH HOH . H 6 HOH A 167 767 767 HOH HOH . H 6 HOH A 168 768 768 HOH HOH . H 6 HOH A 169 769 769 HOH HOH . H 6 HOH A 170 770 770 HOH HOH . H 6 HOH A 171 771 771 HOH HOH . H 6 HOH A 172 772 772 HOH HOH . H 6 HOH A 173 773 773 HOH HOH . H 6 HOH A 174 774 774 HOH HOH . H 6 HOH A 175 775 775 HOH HOH . H 6 HOH A 176 776 776 HOH HOH . H 6 HOH A 177 777 777 HOH HOH . H 6 HOH A 178 778 778 HOH HOH . H 6 HOH A 179 779 779 HOH HOH . H 6 HOH A 180 780 780 HOH HOH . H 6 HOH A 181 781 781 HOH HOH . H 6 HOH A 182 782 782 HOH HOH . H 6 HOH A 183 783 783 HOH HOH . H 6 HOH A 184 784 784 HOH HOH . H 6 HOH A 185 785 785 HOH HOH . H 6 HOH A 186 786 786 HOH HOH . H 6 HOH A 187 787 787 HOH HOH . H 6 HOH A 188 788 788 HOH HOH . H 6 HOH A 189 789 789 HOH HOH . H 6 HOH A 190 790 790 HOH HOH . H 6 HOH A 191 791 791 HOH HOH . H 6 HOH A 192 792 792 HOH HOH . H 6 HOH A 193 793 793 HOH HOH . H 6 HOH A 194 794 794 HOH HOH . H 6 HOH A 195 795 795 HOH HOH . H 6 HOH A 196 796 796 HOH HOH . H 6 HOH A 197 797 797 HOH HOH . H 6 HOH A 198 798 798 HOH HOH . H 6 HOH A 199 799 799 HOH HOH . H 6 HOH A 200 800 800 HOH HOH . H 6 HOH A 201 801 801 HOH HOH . H 6 HOH A 202 802 802 HOH HOH . H 6 HOH A 203 803 803 HOH HOH . H 6 HOH A 204 804 804 HOH HOH . H 6 HOH A 205 805 805 HOH HOH . H 6 HOH A 206 806 806 HOH HOH . H 6 HOH A 207 807 807 HOH HOH . H 6 HOH A 208 808 808 HOH HOH . H 6 HOH A 209 809 809 HOH HOH . H 6 HOH A 210 810 810 HOH HOH . H 6 HOH A 211 811 811 HOH HOH . H 6 HOH A 212 812 812 HOH HOH . H 6 HOH A 213 813 813 HOH HOH . H 6 HOH A 214 814 814 HOH HOH . H 6 HOH A 215 815 815 HOH HOH . H 6 HOH A 216 816 816 HOH HOH . H 6 HOH A 217 817 817 HOH HOH . H 6 HOH A 218 818 818 HOH HOH . H 6 HOH A 219 819 819 HOH HOH . H 6 HOH A 220 820 820 HOH HOH . H 6 HOH A 221 821 821 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 P AMP . . . C 3 4.083 33.58 4.418 1 67.25 ? P AMP 501 A 1 HETATM 2 O O1P AMP . . . C 3 4.939 34.753 4.603 1 72.14 ? O1P AMP 501 A 1 HETATM 3 O O2P AMP . . . C 3 2.832 33.655 5.18 1 66.28 ? O2P AMP 501 A 1 HETATM 4 O O5' AMP . . . C 3 3.626 33.779 2.934 1 71.11 ? O5' AMP 501 A 1 HETATM 5 C C5' AMP . . . C 3 2.672 32.893 2.399 1 66.64 ? C5' AMP 501 A 1 HETATM 6 C C4' AMP . . . C 3 2.591 33.128 0.917 1 68.06 ? C4' AMP 501 A 1 HETATM 7 O O4' AMP . . . C 3 3.833 32.932 0.276 1 69.06 ? O4' AMP 501 A 1 HETATM 8 C C3' AMP . . . C 3 1.657 32.127 0.302 1 76.62 ? C3' AMP 501 A 1 HETATM 9 O O3' AMP . . . C 3 0.357 32.701 0.212 1 84.89 ? O3' AMP 501 A 1 HETATM 10 C C2' AMP . . . C 3 2.187 31.963 -1.085 1 67.97 ? C2' AMP 501 A 1 HETATM 11 O O2' AMP . . . C 3 1.495 32.937 -1.83 1 68.35 ? O2' AMP 501 A 1 HETATM 12 C C1' AMP . . . C 3 3.622 32.387 -1.012 1 66 ? C1' AMP 501 A 1 HETATM 13 N N9 AMP . . . C 3 4.502 31.236 -1.181 1 62.35 ? N9 AMP 501 A 1 HETATM 14 C C8 AMP . . . C 3 5.074 30.558 -0.191 1 59.33 ? C8 AMP 501 A 1 HETATM 15 N N7 AMP . . . C 3 5.842 29.563 -0.666 1 62 ? N7 AMP 501 A 1 HETATM 16 C C5 AMP . . . C 3 5.772 29.619 -2 1 62.51 ? C5 AMP 501 A 1 HETATM 17 C C6 AMP . . . C 3 6.332 28.862 -3.134 1 58.73 ? C6 AMP 501 A 1 HETATM 18 N N6 AMP . . . C 3 7.143 27.838 -2.904 1 54.54 ? N6 AMP 501 A 1 HETATM 19 N N1 AMP . . . C 3 6.017 29.211 -4.383 1 50.28 ? N1 AMP 501 A 1 HETATM 20 C C2 AMP . . . C 3 5.2 30.229 -4.592 1 54.66 ? C2 AMP 501 A 1 HETATM 21 N N3 AMP . . . C 3 4.643 30.972 -3.634 1 57.75 ? N3 AMP 501 A 1 HETATM 22 C C4 AMP . . . C 3 4.886 30.725 -2.336 1 63.93 ? C4 AMP 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #