data_4I2H # _model_server_result.job_id XdWomZVz1NwtEUw3VgSY3A _model_server_result.datetime_utc '2024-11-13 04:26:22' _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 4i2h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":605}' # _entry.id 4I2H # _exptl.entry_id 4I2H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 4I2H _cell.length_a 47.112 _cell.length_b 85.264 _cell.length_c 115.085 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4I2H _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 6 _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 A O THR 143 A THR 253 1_555 D NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A O VAL 145 A VAL 255 1_555 D NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc3 A O VAL 148 A VAL 258 1_555 D NA NA . A NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc4 A OD1 ASP 233 A ASP 343 1_555 C MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc5 A OD2 ASP 233 A ASP 343 1_555 E ZN ZN . A ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 A OD2 ASP 235 A ASP 345 1_555 C MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc7 A OD1 ASP 235 A ASP 345 1_555 E ZN ZN . A ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc8 A OD2 ASP 324 A ASP 434 1_555 E ZN ZN . A ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc9 A OD2 ASP 363 A ASP 473 1_555 F ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc10 A ND1 HIS 365 A HIS 475 1_555 F ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc11 C MG MG . A MG 601 1_555 G O3B APC . A APC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc12 C MG MG . A MG 601 1_555 G O1A APC . A APC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc13 C MG MG . A MG 601 1_555 H O HOH . A HOH 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc14 D NA NA . A NA 602 1_555 B OP1 DA 2 C DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc15 E ZN ZN . A ZN 603 1_555 G O1A APC . A APC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 4I2H _atom_sites.fract_transf_matrix[1][1] 0.021226 _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] 0.011728 _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] 0.008689 _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 3 MG A 1 601 1 MG MG . D 4 NA A 1 602 1 NA NA . E 5 ZN A 1 603 1 ZN ZN . F 5 ZN A 1 604 2 ZN ZN . G 6 APC A 1 605 1 APC APC . H 7 HOH A 1 701 1 HOH HOH . H 7 HOH A 2 702 2 HOH HOH . H 7 HOH A 3 703 3 HOH HOH . H 7 HOH A 4 704 4 HOH HOH . H 7 HOH A 5 705 5 HOH HOH . H 7 HOH A 6 706 6 HOH HOH . H 7 HOH A 7 707 7 HOH HOH . H 7 HOH A 8 708 8 HOH HOH . H 7 HOH A 9 709 9 HOH HOH . H 7 HOH A 10 710 10 HOH HOH . H 7 HOH A 11 711 11 HOH HOH . H 7 HOH A 12 712 12 HOH HOH . H 7 HOH A 13 713 13 HOH HOH . H 7 HOH A 14 714 14 HOH HOH . H 7 HOH A 15 715 15 HOH HOH . H 7 HOH A 16 716 16 HOH HOH . H 7 HOH A 17 717 17 HOH HOH . H 7 HOH A 18 718 18 HOH HOH . H 7 HOH A 19 719 19 HOH HOH . H 7 HOH A 20 720 20 HOH HOH . H 7 HOH A 21 721 21 HOH HOH . H 7 HOH A 22 722 22 HOH HOH . H 7 HOH A 23 723 23 HOH HOH . H 7 HOH A 24 724 24 HOH HOH . H 7 HOH A 25 725 25 HOH HOH . H 7 HOH A 26 726 26 HOH HOH . H 7 HOH A 27 727 27 HOH HOH . H 7 HOH A 28 728 28 HOH HOH . H 7 HOH A 29 729 29 HOH HOH . H 7 HOH A 30 730 30 HOH HOH . H 7 HOH A 31 731 31 HOH HOH . H 7 HOH A 32 732 32 HOH HOH . H 7 HOH A 33 733 34 HOH HOH . H 7 HOH A 34 734 35 HOH HOH . H 7 HOH A 35 735 36 HOH HOH . H 7 HOH A 36 736 37 HOH HOH . H 7 HOH A 37 737 38 HOH HOH . H 7 HOH A 38 738 39 HOH HOH . H 7 HOH A 39 739 40 HOH HOH . H 7 HOH A 40 740 41 HOH HOH . H 7 HOH A 41 741 42 HOH HOH . H 7 HOH A 42 742 43 HOH HOH . H 7 HOH A 43 743 44 HOH HOH . H 7 HOH A 44 744 45 HOH HOH . H 7 HOH A 45 745 46 HOH HOH . H 7 HOH A 46 746 47 HOH HOH . H 7 HOH A 47 747 48 HOH HOH . H 7 HOH A 48 748 49 HOH HOH . H 7 HOH A 49 749 50 HOH HOH . H 7 HOH A 50 750 51 HOH HOH . H 7 HOH A 51 751 52 HOH HOH . H 7 HOH A 52 752 53 HOH HOH . H 7 HOH A 53 753 54 HOH HOH . H 7 HOH A 54 754 55 HOH HOH . H 7 HOH A 55 755 56 HOH HOH . H 7 HOH A 56 756 57 HOH HOH . H 7 HOH A 57 757 58 HOH HOH . H 7 HOH A 58 758 59 HOH HOH . H 7 HOH A 59 759 60 HOH HOH . H 7 HOH A 60 760 61 HOH HOH . H 7 HOH A 61 761 62 HOH HOH . H 7 HOH A 62 762 63 HOH HOH . H 7 HOH A 63 763 64 HOH HOH . H 7 HOH A 64 764 65 HOH HOH . H 7 HOH A 65 765 66 HOH HOH . H 7 HOH A 66 766 67 HOH HOH . H 7 HOH A 67 767 68 HOH HOH . H 7 HOH A 68 768 69 HOH HOH . H 7 HOH A 69 769 70 HOH HOH . H 7 HOH A 70 770 71 HOH HOH . H 7 HOH A 71 771 72 HOH HOH . H 7 HOH A 72 772 73 HOH HOH . H 7 HOH A 73 773 74 HOH HOH . H 7 HOH A 74 774 75 HOH HOH . H 7 HOH A 75 775 76 HOH HOH . H 7 HOH A 76 776 77 HOH HOH . H 7 HOH A 77 777 78 HOH HOH . H 7 HOH A 78 778 79 HOH HOH . H 7 HOH A 79 779 80 HOH HOH . H 7 HOH A 80 780 81 HOH HOH . H 7 HOH A 81 781 82 HOH HOH . H 7 HOH A 82 782 83 HOH HOH . H 7 HOH A 83 783 84 HOH HOH . H 7 HOH A 84 784 85 HOH HOH . H 7 HOH A 85 785 86 HOH HOH . H 7 HOH A 86 786 87 HOH HOH . H 7 HOH A 87 787 88 HOH HOH . H 7 HOH A 88 788 89 HOH HOH . H 7 HOH A 89 789 90 HOH HOH . H 7 HOH A 90 790 91 HOH HOH . H 7 HOH A 91 791 93 HOH HOH . H 7 HOH A 92 792 94 HOH HOH . H 7 HOH A 93 793 95 HOH HOH . H 7 HOH A 94 794 96 HOH HOH . H 7 HOH A 95 795 97 HOH HOH . H 7 HOH A 96 796 98 HOH HOH . H 7 HOH A 97 797 99 HOH HOH . H 7 HOH A 98 798 100 HOH HOH . H 7 HOH A 99 799 101 HOH HOH . H 7 HOH A 100 800 102 HOH HOH . H 7 HOH A 101 801 103 HOH HOH . H 7 HOH A 102 802 104 HOH HOH . H 7 HOH A 103 803 105 HOH HOH . H 7 HOH A 104 804 106 HOH HOH . H 7 HOH A 105 805 107 HOH HOH . H 7 HOH A 106 806 108 HOH HOH . H 7 HOH A 107 807 109 HOH HOH . H 7 HOH A 108 808 110 HOH HOH . H 7 HOH A 109 809 111 HOH HOH . H 7 HOH A 110 810 112 HOH HOH . H 7 HOH A 111 811 113 HOH HOH . H 7 HOH A 112 812 114 HOH HOH . H 7 HOH A 113 813 115 HOH HOH . H 7 HOH A 114 814 116 HOH HOH . H 7 HOH A 115 815 117 HOH HOH . H 7 HOH A 116 816 118 HOH HOH . H 7 HOH A 117 817 119 HOH HOH . H 7 HOH A 118 818 120 HOH HOH . H 7 HOH A 119 819 121 HOH HOH . H 7 HOH A 120 820 122 HOH HOH . H 7 HOH A 121 821 123 HOH HOH . H 7 HOH A 122 822 124 HOH HOH . H 7 HOH A 123 823 125 HOH HOH . H 7 HOH A 124 824 126 HOH HOH . H 7 HOH A 125 825 127 HOH HOH . H 7 HOH A 126 826 128 HOH HOH . H 7 HOH A 127 827 129 HOH HOH . H 7 HOH A 128 828 130 HOH HOH . H 7 HOH A 129 829 131 HOH HOH . H 7 HOH A 130 830 132 HOH HOH . H 7 HOH A 131 831 133 HOH HOH . H 7 HOH A 132 832 134 HOH HOH . H 7 HOH A 133 833 135 HOH HOH . H 7 HOH A 134 834 136 HOH HOH . H 7 HOH A 135 835 137 HOH HOH . H 7 HOH A 136 836 138 HOH HOH . H 7 HOH A 137 837 139 HOH HOH . H 7 HOH A 138 838 140 HOH HOH . H 7 HOH A 139 839 141 HOH HOH . H 7 HOH A 140 840 142 HOH HOH . H 7 HOH A 141 841 143 HOH HOH . H 7 HOH A 142 842 144 HOH HOH . H 7 HOH A 143 843 145 HOH HOH . H 7 HOH A 144 844 146 HOH HOH . H 7 HOH A 145 845 147 HOH HOH . H 7 HOH A 146 846 148 HOH HOH . H 7 HOH A 147 847 149 HOH HOH . H 7 HOH A 148 848 150 HOH HOH . H 7 HOH A 149 849 151 HOH HOH . H 7 HOH A 150 850 152 HOH HOH . H 7 HOH A 151 851 153 HOH HOH . H 7 HOH A 152 852 154 HOH HOH . I 7 HOH C 1 101 33 HOH HOH . I 7 HOH C 2 102 92 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 PG APC . . . G 6 19.814 -8.837 -23.577 1 148.29 ? PG APC 605 A 1 HETATM 2 O O1G APC . . . G 6 19.435 -10.019 -24.615 1 146.93 ? O1G APC 605 A 1 HETATM 3 O O2G APC . . . G 6 20.553 -7.748 -24.265 1 147.75 ? O2G APC 605 A 1 HETATM 4 O O3G APC . . . G 6 20.827 -9.478 -22.499 1 149.58 ? O3G APC 605 A 1 HETATM 5 P PB APC . . . G 6 17.807 -8.374 -21.401 1 144.32 ? PB APC 605 A 1 HETATM 6 O O1B APC . . . G 6 17.227 -7.106 -20.902 1 142.04 ? O1B APC 605 A 1 HETATM 7 O O2B APC . . . G 6 18.975 -8.663 -20.312 1 142.97 ? O2B APC 605 A 1 HETATM 8 O O3B APC . . . G 6 18.426 -8.122 -22.941 1 147.66 ? O3B APC 605 A 1 HETATM 9 P PA APC . . . G 6 15.124 -10.033 -22.722 1 141.95 ? PA APC 605 A 1 HETATM 10 O O1A APC . . . G 6 15.734 -9.727 -24.158 1 141.92 ? O1A APC 605 A 1 HETATM 11 O O2A APC . . . G 6 14.593 -11.428 -22.694 1 141.24 ? O2A APC 605 A 1 HETATM 12 C C3A APC . . . G 6 16.511 -9.77 -21.442 1 143.83 ? C3A APC 605 A 1 HETATM 13 O O5' APC . . . G 6 13.841 -9.049 -22.506 1 140.54 ? O5' APC 605 A 1 HETATM 14 C C5' APC . . . G 6 14.304 -7.704 -22.134 1 139.14 ? C5' APC 605 A 1 HETATM 15 C C4' APC . . . G 6 13.903 -7.004 -20.795 1 136.17 ? C4' APC 605 A 1 HETATM 16 O O4' APC . . . G 6 12.492 -6.81 -20.528 1 134.64 ? O4' APC 605 A 1 HETATM 17 C C3' APC . . . G 6 14.549 -7.607 -19.542 1 134.75 ? C3' APC 605 A 1 HETATM 18 O O3' APC . . . G 6 15.397 -6.689 -18.846 1 134.59 ? O3' APC 605 A 1 HETATM 19 C C2' APC . . . G 6 13.363 -8.169 -18.752 1 133.04 ? C2' APC 605 A 1 HETATM 20 O O2' APC . . . G 6 13.592 -8.147 -17.352 1 132.15 ? O2' APC 605 A 1 HETATM 21 C C1' APC . . . G 6 12.081 -7.506 -19.32 1 132.98 ? C1' APC 605 A 1 HETATM 22 N N9 APC . . . G 6 11.2 -8.552 -19.82 1 132.74 ? N9 APC 605 A 1 HETATM 23 C C8 APC . . . G 6 11.56 -9.454 -20.793 1 133.93 ? C8 APC 605 A 1 HETATM 24 N N7 APC . . . G 6 10.636 -10.296 -21.081 1 134.21 ? N7 APC 605 A 1 HETATM 25 C C5 APC . . . G 6 9.573 -10.001 -20.3 1 133.37 ? C5 APC 605 A 1 HETATM 26 C C6 APC . . . G 6 8.285 -10.587 -20.19 1 131.58 ? C6 APC 605 A 1 HETATM 27 N N6 APC . . . G 6 8.005 -11.678 -21.018 1 130.76 ? N6 APC 605 A 1 HETATM 28 N N1 APC . . . G 6 7.413 -10.045 -19.288 1 130.18 ? N1 APC 605 A 1 HETATM 29 C C2 APC . . . G 6 7.766 -8.981 -18.529 1 130.19 ? C2 APC 605 A 1 HETATM 30 N N3 APC . . . G 6 8.978 -8.387 -18.598 1 130.93 ? N3 APC 605 A 1 HETATM 31 C C4 APC . . . G 6 9.907 -8.861 -19.466 1 132.45 ? C4 APC 605 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #