data_6V89 # _model_server_result.job_id fz-kDVFBVfQeGFMK0mhUxQ _model_server_result.datetime_utc '2024-12-30 17:45:27' _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 6v89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6V89 # _exptl.entry_id 6V89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _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 120 _cell.entry_id 6V89 _cell.length_a 88.944 _cell.length_b 88.944 _cell.length_c 163.72 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V89 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall 'P 64 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 12_564 x,x-y+1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -44.472 77.027764 -54.573333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 CA CA . A CA 504 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc2 E CA CA . A CA 504 1_555 F O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc3 E CA CA . A CA 504 1_555 F O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? metalc ? metalc4 E CA CA . A CA 504 1_555 F O HOH . A HOH 657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc5 E CA CA . A CA 504 1_555 F O HOH . A HOH 672 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc6 E CA CA . A CA 504 1_555 F O HOH . A HOH 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? # _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 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 6V89 _atom_sites.fract_transf_matrix[1][1] 0.011243 _atom_sites.fract_transf_matrix[1][2] 0.006491 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012982 _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] 0.006108 _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 AMP A 1 501 501 AMP AMP . C 3 CL A 1 502 2 CL CL . D 3 CL A 1 503 3 CL CL . E 4 CA A 1 504 1 CA CA . F 5 HOH A 1 601 78 HOH HOH . F 5 HOH A 2 602 57 HOH HOH . F 5 HOH A 3 603 3 HOH HOH . F 5 HOH A 4 604 27 HOH HOH . F 5 HOH A 5 605 45 HOH HOH . F 5 HOH A 6 606 13 HOH HOH . F 5 HOH A 7 607 70 HOH HOH . F 5 HOH A 8 608 82 HOH HOH . F 5 HOH A 9 609 37 HOH HOH . F 5 HOH A 10 610 79 HOH HOH . F 5 HOH A 11 611 49 HOH HOH . F 5 HOH A 12 612 60 HOH HOH . F 5 HOH A 13 613 95 HOH HOH . F 5 HOH A 14 614 122 HOH HOH . F 5 HOH A 15 615 114 HOH HOH . F 5 HOH A 16 616 43 HOH HOH . F 5 HOH A 17 617 25 HOH HOH . F 5 HOH A 18 618 44 HOH HOH . F 5 HOH A 19 619 34 HOH HOH . F 5 HOH A 20 620 104 HOH HOH . F 5 HOH A 21 621 26 HOH HOH . F 5 HOH A 22 622 42 HOH HOH . F 5 HOH A 23 623 22 HOH HOH . F 5 HOH A 24 624 64 HOH HOH . F 5 HOH A 25 625 151 HOH HOH . F 5 HOH A 26 626 24 HOH HOH . F 5 HOH A 27 627 10 HOH HOH . F 5 HOH A 28 628 39 HOH HOH . F 5 HOH A 29 629 19 HOH HOH . F 5 HOH A 30 630 134 HOH HOH . F 5 HOH A 31 631 118 HOH HOH . F 5 HOH A 32 632 20 HOH HOH . F 5 HOH A 33 633 116 HOH HOH . F 5 HOH A 34 634 139 HOH HOH . F 5 HOH A 35 635 11 HOH HOH . F 5 HOH A 36 636 15 HOH HOH . F 5 HOH A 37 637 130 HOH HOH . F 5 HOH A 38 638 9 HOH HOH . F 5 HOH A 39 639 33 HOH HOH . F 5 HOH A 40 640 41 HOH HOH . F 5 HOH A 41 641 128 HOH HOH . F 5 HOH A 42 642 98 HOH HOH . F 5 HOH A 43 643 16 HOH HOH . F 5 HOH A 44 644 28 HOH HOH . F 5 HOH A 45 645 17 HOH HOH . F 5 HOH A 46 646 91 HOH HOH . F 5 HOH A 47 647 5 HOH HOH . F 5 HOH A 48 648 146 HOH HOH . F 5 HOH A 49 649 100 HOH HOH . F 5 HOH A 50 650 18 HOH HOH . F 5 HOH A 51 651 48 HOH HOH . F 5 HOH A 52 652 14 HOH HOH . F 5 HOH A 53 653 12 HOH HOH . F 5 HOH A 54 654 6 HOH HOH . F 5 HOH A 55 655 107 HOH HOH . F 5 HOH A 56 656 145 HOH HOH . F 5 HOH A 57 657 68 HOH HOH . F 5 HOH A 58 658 137 HOH HOH . F 5 HOH A 59 659 46 HOH HOH . F 5 HOH A 60 660 112 HOH HOH . F 5 HOH A 61 661 94 HOH HOH . F 5 HOH A 62 662 81 HOH HOH . F 5 HOH A 63 663 35 HOH HOH . F 5 HOH A 64 664 30 HOH HOH . F 5 HOH A 65 665 120 HOH HOH . F 5 HOH A 66 666 53 HOH HOH . F 5 HOH A 67 667 38 HOH HOH . F 5 HOH A 68 668 149 HOH HOH . F 5 HOH A 69 669 84 HOH HOH . F 5 HOH A 70 670 72 HOH HOH . F 5 HOH A 71 671 121 HOH HOH . F 5 HOH A 72 672 147 HOH HOH . F 5 HOH A 73 673 21 HOH HOH . F 5 HOH A 74 674 148 HOH HOH . F 5 HOH A 75 675 126 HOH HOH . F 5 HOH A 76 676 23 HOH HOH . F 5 HOH A 77 677 51 HOH HOH . F 5 HOH A 78 678 66 HOH HOH . F 5 HOH A 79 679 97 HOH HOH . F 5 HOH A 80 680 96 HOH HOH . F 5 HOH A 81 681 47 HOH HOH . F 5 HOH A 82 682 77 HOH HOH . F 5 HOH A 83 683 90 HOH HOH . F 5 HOH A 84 684 88 HOH HOH . F 5 HOH A 85 685 162 HOH HOH . F 5 HOH A 86 686 63 HOH HOH . F 5 HOH A 87 687 135 HOH HOH . F 5 HOH A 88 688 65 HOH HOH . F 5 HOH A 89 689 124 HOH HOH . F 5 HOH A 90 690 85 HOH HOH . F 5 HOH A 91 691 99 HOH HOH . F 5 HOH A 92 692 127 HOH HOH . F 5 HOH A 93 693 119 HOH HOH . F 5 HOH A 94 694 93 HOH HOH . F 5 HOH A 95 695 74 HOH HOH . F 5 HOH A 96 696 62 HOH HOH . F 5 HOH A 97 697 108 HOH HOH . F 5 HOH A 98 698 123 HOH HOH . F 5 HOH A 99 699 117 HOH HOH . F 5 HOH A 100 700 102 HOH HOH . F 5 HOH A 101 701 111 HOH HOH . F 5 HOH A 102 702 153 HOH HOH . F 5 HOH A 103 703 115 HOH HOH . F 5 HOH A 104 704 67 HOH HOH . F 5 HOH A 105 705 54 HOH HOH . F 5 HOH A 106 706 71 HOH HOH . F 5 HOH A 107 707 89 HOH HOH . F 5 HOH A 108 708 8 HOH HOH . F 5 HOH A 109 709 58 HOH HOH . F 5 HOH A 110 710 113 HOH HOH . F 5 HOH A 111 711 182 HOH HOH . F 5 HOH A 112 712 50 HOH HOH . F 5 HOH A 113 713 69 HOH HOH . F 5 HOH A 114 714 75 HOH HOH . F 5 HOH A 115 715 141 HOH HOH . F 5 HOH A 116 716 80 HOH HOH . F 5 HOH A 117 717 154 HOH HOH . F 5 HOH A 118 718 183 HOH HOH . F 5 HOH A 119 719 76 HOH HOH . F 5 HOH A 120 720 156 HOH HOH . F 5 HOH A 121 721 106 HOH HOH . F 5 HOH A 122 722 109 HOH HOH . F 5 HOH A 123 723 52 HOH HOH . F 5 HOH A 124 724 129 HOH HOH . F 5 HOH A 125 725 32 HOH HOH . F 5 HOH A 126 726 184 HOH HOH . F 5 HOH A 127 727 157 HOH HOH . F 5 HOH A 128 728 131 HOH HOH . F 5 HOH A 129 729 176 HOH HOH . F 5 HOH A 130 730 59 HOH HOH . F 5 HOH A 131 731 158 HOH HOH . F 5 HOH A 132 732 159 HOH HOH . F 5 HOH A 133 733 175 HOH HOH . F 5 HOH A 134 734 36 HOH HOH . F 5 HOH A 135 735 165 HOH HOH . F 5 HOH A 136 736 174 HOH HOH . F 5 HOH A 137 737 86 HOH HOH . F 5 HOH A 138 738 177 HOH HOH . F 5 HOH A 139 739 166 HOH HOH . F 5 HOH A 140 740 56 HOH HOH . F 5 HOH A 141 741 164 HOH HOH . F 5 HOH A 142 742 181 HOH HOH . F 5 HOH A 143 743 180 HOH HOH . F 5 HOH A 144 744 87 HOH HOH . F 5 HOH A 145 745 161 HOH HOH . F 5 HOH A 146 746 160 HOH HOH . F 5 HOH A 147 747 178 HOH HOH . F 5 HOH A 148 748 167 HOH HOH . F 5 HOH A 149 749 169 HOH HOH . F 5 HOH A 150 750 179 HOH HOH . F 5 HOH A 151 751 168 HOH HOH . F 5 HOH A 152 752 170 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 . . . B 2 -3.937 25.677 -26.519 1 54.3 ? P AMP 501 A 1 HETATM 2 O O1P AMP . . . B 2 -3.349 27.066 -26.603 1 57.8 ? O1P AMP 501 A 1 HETATM 3 O O2P AMP . . . B 2 -5.172 25.585 -25.652 1 52.23 ? O2P AMP 501 A 1 HETATM 4 O O3P AMP . . . B 2 -2.925 24.587 -26.261 1 55.41 ? O3P AMP 501 A 1 HETATM 5 O O5' AMP . . . B 2 -4.47 25.388 -27.994 1 50.93 ? O5' AMP 501 A 1 HETATM 6 C C5' AMP . . . B 2 -3.595 25.393 -29.121 1 49.88 ? C5' AMP 501 A 1 HETATM 7 C C4' AMP . . . B 2 -4.345 25.071 -30.391 1 49.8 ? C4' AMP 501 A 1 HETATM 8 O O4' AMP . . . B 2 -3.484 25.257 -31.545 1 49.59 ? O4' AMP 501 A 1 HETATM 9 C C3' AMP . . . B 2 -4.875 23.631 -30.472 1 51.19 ? C3' AMP 501 A 1 HETATM 10 O O3' AMP . . . B 2 -6.267 23.638 -30.788 1 52.7 ? O3' AMP 501 A 1 HETATM 11 C C2' AMP . . . B 2 -4.073 23.004 -31.622 1 51.04 ? C2' AMP 501 A 1 HETATM 12 O O2' AMP . . . B 2 -4.766 22.026 -32.368 1 51.32 ? O2' AMP 501 A 1 HETATM 13 C C1' AMP . . . B 2 -3.727 24.221 -32.466 1 49.95 ? C1' AMP 501 A 1 HETATM 14 N N9 AMP . . . B 2 -2.551 24.053 -33.32 1 48.96 ? N9 AMP 501 A 1 HETATM 15 C C8 AMP . . . B 2 -1.427 23.373 -33.028 1 48.86 ? C8 AMP 501 A 1 HETATM 16 N N7 AMP . . . B 2 -0.555 23.427 -34.068 1 49.29 ? N7 AMP 501 A 1 HETATM 17 C C5 AMP . . . B 2 -1.132 24.147 -35.047 1 48.93 ? C5 AMP 501 A 1 HETATM 18 C C6 AMP . . . B 2 -0.77 24.593 -36.411 1 49.3 ? C6 AMP 501 A 1 HETATM 19 N N6 AMP . . . B 2 0.425 24.268 -36.956 1 49.99 ? N6 AMP 501 A 1 HETATM 20 N N1 AMP . . . B 2 -1.672 25.335 -37.092 1 49.42 ? N1 AMP 501 A 1 HETATM 21 C C2 AMP . . . B 2 -2.867 25.672 -36.572 1 47.93 ? C2 AMP 501 A 1 HETATM 22 N N3 AMP . . . B 2 -3.255 25.299 -35.341 1 47.54 ? N3 AMP 501 A 1 HETATM 23 C C4 AMP . . . B 2 -2.451 24.55 -34.551 1 48.37 ? C4 AMP 501 A 1 HETATM 24 H "H5'1" AMP . . . B 2 -2.802 24.657 -28.97 1 59.83 ? "H5'1" AMP 501 A 1 HETATM 25 H "H5'2" AMP . . . B 2 -3.127 26.375 -29.213 1 59.83 ? "H5'2" AMP 501 A 1 HETATM 26 H H4' AMP . . . B 2 -5.189 25.77 -30.477 1 59.74 ? H4' AMP 501 A 1 HETATM 27 H H3' AMP . . . B 2 -4.665 23.1 -29.534 1 61.41 ? H3' AMP 501 A 1 HETATM 28 H HO3' AMP . . . B 2 -6.606 22.733 -30.768 1 63.22 ? HO3' AMP 501 A 1 HETATM 29 H H2' AMP . . . B 2 -3.145 22.582 -31.21 1 61.23 ? H2' AMP 501 A 1 HETATM 30 H HO2' AMP . . . B 2 -4.915 21.245 -31.817 1 61.56 ? HO2' AMP 501 A 1 HETATM 31 H H1' AMP . . . B 2 -4.591 24.477 -33.096 1 59.92 ? H1' AMP 501 A 1 HETATM 32 H H8 AMP . . . B 2 -1.243 22.855 -32.095 1 58.61 ? H8 AMP 501 A 1 HETATM 33 H HN61 AMP . . . B 2 0.657 24.58 -37.888 1 59.97 ? HN61 AMP 501 A 1 HETATM 34 H HN62 AMP . . . B 2 1.082 23.714 -36.429 1 59.97 ? HN62 AMP 501 A 1 HETATM 35 H H2 AMP . . . B 2 -3.544 26.268 -37.172 1 57.49 ? H2 AMP 501 A 1 # _model_server_stats.io_time_ms 124 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #