data_6M4I # _model_server_result.job_id 3fpT7cmC1hUrtLzO8PuxEA _model_server_result.datetime_utc '2024-11-13 22:08:57' _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 6m4i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":600}' # _entry.id 6M4I # _exptl.entry_id 6M4I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 100.85 _cell.angle_gamma 90 _cell.entry_id 6M4I _cell.length_a 96.825 _cell.length_b 82.839 _cell.length_c 49.372 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M4I _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,D,G 1 1 B,E,F,H 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 E N 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 A OG1 THR 99 A THR 93 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc2 C O2B ADP . A ADP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc3 D MG MG . A MG 601 1_555 G O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc4 D MG MG . A MG 601 1_555 G O HOH . A HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 D MG MG . A MG 601 1_555 G O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc6 D MG MG . A MG 601 1_555 G O HOH . A HOH 779 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc7 B OG1 THR 99 B THR 93 1_555 F MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc8 E O2B ADP . B ADP 600 1_555 F MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc9 F MG MG . B MG 601 1_555 H O HOH . B HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc10 F MG MG . B MG 601 1_555 H O HOH . B HOH 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc11 F MG MG . B MG 601 1_555 H O HOH . B HOH 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc12 F MG MG . B MG 601 1_555 H O HOH . B HOH 739 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6M4I _atom_sites.fract_transf_matrix[1][1] 0.010328 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001979 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012072 _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] 0.020623 _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 ADP A 1 600 600 ADP ADP . D 3 MG A 1 601 601 MG MG . E 2 ADP B 1 600 600 ADP ADP . F 3 MG B 1 601 601 MG MG . G 4 HOH A 1 701 137 HOH HOH . G 4 HOH A 2 702 40 HOH HOH . G 4 HOH A 3 703 8 HOH HOH . G 4 HOH A 4 704 77 HOH HOH . G 4 HOH A 5 705 58 HOH HOH . G 4 HOH A 6 706 90 HOH HOH . G 4 HOH A 7 707 32 HOH HOH . G 4 HOH A 8 708 51 HOH HOH . G 4 HOH A 9 709 111 HOH HOH . G 4 HOH A 10 710 18 HOH HOH . G 4 HOH A 11 711 7 HOH HOH . G 4 HOH A 12 712 20 HOH HOH . G 4 HOH A 13 713 59 HOH HOH . G 4 HOH A 14 714 60 HOH HOH . G 4 HOH A 15 715 12 HOH HOH . G 4 HOH A 16 716 47 HOH HOH . G 4 HOH A 17 717 83 HOH HOH . G 4 HOH A 18 718 120 HOH HOH . G 4 HOH A 19 719 22 HOH HOH . G 4 HOH A 20 720 57 HOH HOH . G 4 HOH A 21 721 92 HOH HOH . G 4 HOH A 22 722 118 HOH HOH . G 4 HOH A 23 723 119 HOH HOH . G 4 HOH A 24 724 11 HOH HOH . G 4 HOH A 25 725 44 HOH HOH . G 4 HOH A 26 726 62 HOH HOH . G 4 HOH A 27 727 17 HOH HOH . G 4 HOH A 28 728 48 HOH HOH . G 4 HOH A 29 729 91 HOH HOH . G 4 HOH A 30 730 6 HOH HOH . G 4 HOH A 31 731 139 HOH HOH . G 4 HOH A 32 732 109 HOH HOH . G 4 HOH A 33 733 124 HOH HOH . G 4 HOH A 34 734 85 HOH HOH . G 4 HOH A 35 735 15 HOH HOH . G 4 HOH A 36 736 65 HOH HOH . G 4 HOH A 37 737 66 HOH HOH . G 4 HOH A 38 738 84 HOH HOH . G 4 HOH A 39 739 31 HOH HOH . G 4 HOH A 40 740 16 HOH HOH . G 4 HOH A 41 741 34 HOH HOH . G 4 HOH A 42 742 24 HOH HOH . G 4 HOH A 43 743 14 HOH HOH . G 4 HOH A 44 744 68 HOH HOH . G 4 HOH A 45 745 52 HOH HOH . G 4 HOH A 46 746 122 HOH HOH . G 4 HOH A 47 747 81 HOH HOH . G 4 HOH A 48 748 108 HOH HOH . G 4 HOH A 49 749 43 HOH HOH . G 4 HOH A 50 750 102 HOH HOH . G 4 HOH A 51 751 19 HOH HOH . G 4 HOH A 52 752 25 HOH HOH . G 4 HOH A 53 753 112 HOH HOH . G 4 HOH A 54 754 13 HOH HOH . G 4 HOH A 55 755 82 HOH HOH . G 4 HOH A 56 756 75 HOH HOH . G 4 HOH A 57 757 26 HOH HOH . G 4 HOH A 58 758 114 HOH HOH . G 4 HOH A 59 759 49 HOH HOH . G 4 HOH A 60 760 9 HOH HOH . G 4 HOH A 61 761 23 HOH HOH . G 4 HOH A 62 762 54 HOH HOH . G 4 HOH A 63 763 30 HOH HOH . G 4 HOH A 64 764 4 HOH HOH . G 4 HOH A 65 765 72 HOH HOH . G 4 HOH A 66 766 2 HOH HOH . G 4 HOH A 67 767 87 HOH HOH . G 4 HOH A 68 768 93 HOH HOH . G 4 HOH A 69 769 67 HOH HOH . G 4 HOH A 70 770 113 HOH HOH . G 4 HOH A 71 771 39 HOH HOH . G 4 HOH A 72 772 80 HOH HOH . G 4 HOH A 73 773 86 HOH HOH . G 4 HOH A 74 774 99 HOH HOH . G 4 HOH A 75 775 42 HOH HOH . G 4 HOH A 76 776 10 HOH HOH . G 4 HOH A 77 777 38 HOH HOH . G 4 HOH A 78 778 29 HOH HOH . G 4 HOH A 79 779 73 HOH HOH . G 4 HOH A 80 780 37 HOH HOH . G 4 HOH A 81 781 105 HOH HOH . G 4 HOH A 82 782 97 HOH HOH . G 4 HOH A 83 783 71 HOH HOH . G 4 HOH A 84 784 138 HOH HOH . G 4 HOH A 85 785 50 HOH HOH . G 4 HOH A 86 786 95 HOH HOH . G 4 HOH A 87 787 36 HOH HOH . G 4 HOH A 88 788 96 HOH HOH . G 4 HOH A 89 789 94 HOH HOH . G 4 HOH A 90 790 88 HOH HOH . G 4 HOH A 91 791 21 HOH HOH . G 4 HOH A 92 792 1 HOH HOH . G 4 HOH A 93 793 5 HOH HOH . G 4 HOH A 94 794 53 HOH HOH . G 4 HOH A 95 795 27 HOH HOH . G 4 HOH A 96 796 33 HOH HOH . G 4 HOH A 97 797 78 HOH HOH . G 4 HOH A 98 798 45 HOH HOH . G 4 HOH A 99 799 106 HOH HOH . G 4 HOH A 100 800 135 HOH HOH . H 4 HOH B 1 701 121 HOH HOH . H 4 HOH B 2 702 35 HOH HOH . H 4 HOH B 3 703 103 HOH HOH . H 4 HOH B 4 704 128 HOH HOH . H 4 HOH B 5 705 89 HOH HOH . H 4 HOH B 6 706 46 HOH HOH . H 4 HOH B 7 707 134 HOH HOH . H 4 HOH B 8 708 104 HOH HOH . H 4 HOH B 9 709 41 HOH HOH . H 4 HOH B 10 710 125 HOH HOH . H 4 HOH B 11 711 129 HOH HOH . H 4 HOH B 12 712 126 HOH HOH . H 4 HOH B 13 713 133 HOH HOH . H 4 HOH B 14 714 101 HOH HOH . H 4 HOH B 15 715 69 HOH HOH . H 4 HOH B 16 716 132 HOH HOH . H 4 HOH B 17 717 74 HOH HOH . H 4 HOH B 18 718 136 HOH HOH . H 4 HOH B 19 719 70 HOH HOH . H 4 HOH B 20 720 79 HOH HOH . H 4 HOH B 21 721 63 HOH HOH . H 4 HOH B 22 722 115 HOH HOH . H 4 HOH B 23 723 127 HOH HOH . H 4 HOH B 24 724 76 HOH HOH . H 4 HOH B 25 725 110 HOH HOH . H 4 HOH B 26 726 130 HOH HOH . H 4 HOH B 27 727 131 HOH HOH . H 4 HOH B 28 728 100 HOH HOH . H 4 HOH B 29 729 55 HOH HOH . H 4 HOH B 30 730 117 HOH HOH . H 4 HOH B 31 731 3 HOH HOH . H 4 HOH B 32 732 140 HOH HOH . H 4 HOH B 33 733 116 HOH HOH . H 4 HOH B 34 734 98 HOH HOH . H 4 HOH B 35 735 28 HOH HOH . H 4 HOH B 36 736 61 HOH HOH . H 4 HOH B 37 737 107 HOH HOH . H 4 HOH B 38 738 123 HOH HOH . H 4 HOH B 39 739 64 HOH HOH . H 4 HOH B 40 740 56 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 ADP . . . C 2 55.802 13.181 9.871 1 37.19 ? PB ADP 600 A 1 HETATM 2 O O1B ADP . . . C 2 54.623 12.463 9.332 1 33.75 ? O1B ADP 600 A 1 HETATM 3 O O2B ADP . . . C 2 55.405 14.399 10.731 1 40.64 ? O2B ADP 600 A 1 HETATM 4 O O3B ADP . . . C 2 56.78 12.306 10.533 1 38.74 ? O3B ADP 600 A 1 HETATM 5 P PA ADP . . . C 2 56.883 15.41 8.296 1 41.93 ? PA ADP 600 A 1 HETATM 6 O O1A ADP . . . C 2 55.617 16.171 8.142 1 38.09 ? O1A ADP 600 A 1 HETATM 7 O O2A ADP . . . C 2 57.897 15.873 9.261 1 38.8 ? O2A ADP 600 A 1 HETATM 8 O O3A ADP . . . C 2 56.509 13.873 8.591 1 40.4 ? O3A ADP 600 A 1 HETATM 9 O O5' ADP . . . C 2 57.515 15.289 6.813 1 44.72 ? O5' ADP 600 A 1 HETATM 10 C C5' ADP . . . C 2 58.81 14.69 6.569 1 51.03 ? C5' ADP 600 A 1 HETATM 11 C C4' ADP . . . C 2 59.631 15.581 5.659 1 51.44 ? C4' ADP 600 A 1 HETATM 12 O O4' ADP . . . C 2 59.032 15.638 4.343 1 41.57 ? O4' ADP 600 A 1 HETATM 13 C C3' ADP . . . C 2 59.758 17.041 6.106 1 57.03 ? C3' ADP 600 A 1 HETATM 14 O O3' ADP . . . C 2 61.028 17.563 5.746 1 72.94 ? O3' ADP 600 A 1 HETATM 15 C C2' ADP . . . C 2 58.62 17.719 5.351 1 49.36 ? C2' ADP 600 A 1 HETATM 16 O O2' ADP . . . C 2 58.776 19.095 5.107 1 63.88 ? O2' ADP 600 A 1 HETATM 17 C C1' ADP . . . C 2 58.638 16.96 4.036 1 47.72 ? C1' ADP 600 A 1 HETATM 18 N N9 ADP . . . C 2 57.314 16.934 3.417 1 42.4 ? N9 ADP 600 A 1 HETATM 19 C C8 ADP . . . C 2 56.254 16.203 3.871 1 39.08 ? C8 ADP 600 A 1 HETATM 20 N N7 ADP . . . C 2 55.17 16.35 3.158 1 36.38 ? N7 ADP 600 A 1 HETATM 21 C C5 ADP . . . C 2 55.547 17.216 2.152 1 38.48 ? C5 ADP 600 A 1 HETATM 22 C C6 ADP . . . C 2 54.839 17.729 1.063 1 40.54 ? C6 ADP 600 A 1 HETATM 23 N N6 ADP . . . C 2 53.555 17.443 0.83 1 43.94 ? N6 ADP 600 A 1 HETATM 24 N N1 ADP . . . C 2 55.498 18.579 0.234 1 48.65 ? N1 ADP 600 A 1 HETATM 25 C C2 ADP . . . C 2 56.777 18.859 0.506 1 43.86 ? C2 ADP 600 A 1 HETATM 26 N N3 ADP . . . C 2 57.555 18.411 1.485 1 46.94 ? N3 ADP 600 A 1 HETATM 27 C C4 ADP . . . C 2 56.869 17.584 2.291 1 46.15 ? C4 ADP 600 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #