data_2D7D
#
_model_server_result.job_id            2Os2CcUSW5i45PkwqQiHdw 
_model_server_result.datetime_utc      '2024-12-07 04:42:40' 
_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          2d7d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":662}' 
#
_entry.id    2D7D 
#
_exptl.entry_id    2D7D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-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          90 
_cell.angle_gamma         90 
_cell.entry_id            2D7D 
_cell.length_a            74.231 
_cell.length_b            98.215 
_cell.length_c            95.405 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2D7D 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     2D7D 
_atom_sites.fract_transf_matrix[1][1]    0.013471 
_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]    0.010182 
_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]    0.010482 
_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
D 4 ADP A 1 662 500 ADP ADP . 
E 5 HOH D 1 74 74 HOH HOH . 
F 5 HOH A 1 663 1 HOH HOH . 
F 5 HOH A 2 664 2 HOH HOH . 
F 5 HOH A 3 665 3 HOH HOH . 
F 5 HOH A 4 666 4 HOH HOH . 
F 5 HOH A 5 667 5 HOH HOH . 
F 5 HOH A 6 668 6 HOH HOH . 
F 5 HOH A 7 669 7 HOH HOH . 
F 5 HOH A 8 670 8 HOH HOH . 
F 5 HOH A 9 671 9 HOH HOH . 
F 5 HOH A 10 672 10 HOH HOH . 
F 5 HOH A 11 673 11 HOH HOH . 
F 5 HOH A 12 674 12 HOH HOH . 
F 5 HOH A 13 675 13 HOH HOH . 
F 5 HOH A 14 676 14 HOH HOH . 
F 5 HOH A 15 677 15 HOH HOH . 
F 5 HOH A 16 678 16 HOH HOH . 
F 5 HOH A 17 679 17 HOH HOH . 
F 5 HOH A 18 680 18 HOH HOH . 
F 5 HOH A 19 681 19 HOH HOH . 
F 5 HOH A 20 682 20 HOH HOH . 
F 5 HOH A 21 683 21 HOH HOH . 
F 5 HOH A 22 684 22 HOH HOH . 
F 5 HOH A 23 685 23 HOH HOH . 
F 5 HOH A 24 686 24 HOH HOH . 
F 5 HOH A 25 687 25 HOH HOH . 
F 5 HOH A 26 688 26 HOH HOH . 
F 5 HOH A 27 689 27 HOH HOH . 
F 5 HOH A 28 690 28 HOH HOH . 
F 5 HOH A 29 691 29 HOH HOH . 
F 5 HOH A 30 692 30 HOH HOH . 
F 5 HOH A 31 693 31 HOH HOH . 
F 5 HOH A 32 694 32 HOH HOH . 
F 5 HOH A 33 695 33 HOH HOH . 
F 5 HOH A 34 696 34 HOH HOH . 
F 5 HOH A 35 697 35 HOH HOH . 
F 5 HOH A 36 698 37 HOH HOH . 
F 5 HOH A 37 699 38 HOH HOH . 
F 5 HOH A 38 700 39 HOH HOH . 
F 5 HOH A 39 701 40 HOH HOH . 
F 5 HOH A 40 702 41 HOH HOH . 
F 5 HOH A 41 703 42 HOH HOH . 
F 5 HOH A 42 704 43 HOH HOH . 
F 5 HOH A 43 705 44 HOH HOH . 
F 5 HOH A 44 706 45 HOH HOH . 
F 5 HOH A 45 707 46 HOH HOH . 
F 5 HOH A 46 708 47 HOH HOH . 
F 5 HOH A 47 709 48 HOH HOH . 
F 5 HOH A 48 710 49 HOH HOH . 
F 5 HOH A 49 711 50 HOH HOH . 
F 5 HOH A 50 712 51 HOH HOH . 
F 5 HOH A 51 713 52 HOH HOH . 
F 5 HOH A 52 714 53 HOH HOH . 
F 5 HOH A 53 715 54 HOH HOH . 
F 5 HOH A 54 716 55 HOH HOH . 
F 5 HOH A 55 717 56 HOH HOH . 
F 5 HOH A 56 718 57 HOH HOH . 
F 5 HOH A 57 719 58 HOH HOH . 
F 5 HOH A 58 720 59 HOH HOH . 
F 5 HOH A 59 721 61 HOH HOH . 
F 5 HOH A 60 722 62 HOH HOH . 
F 5 HOH A 61 723 63 HOH HOH . 
F 5 HOH A 62 724 64 HOH HOH . 
F 5 HOH A 63 725 66 HOH HOH . 
F 5 HOH A 64 726 67 HOH HOH . 
F 5 HOH A 65 727 68 HOH HOH . 
F 5 HOH A 66 728 69 HOH HOH . 
F 5 HOH A 67 729 70 HOH HOH . 
F 5 HOH A 68 730 71 HOH HOH . 
F 5 HOH A 69 731 72 HOH HOH . 
F 5 HOH A 70 732 73 HOH HOH . 
F 5 HOH A 71 733 75 HOH HOH . 
F 5 HOH A 72 734 76 HOH HOH . 
F 5 HOH A 73 735 77 HOH HOH . 
F 5 HOH A 74 736 78 HOH HOH . 
F 5 HOH A 75 737 79 HOH HOH . 
F 5 HOH A 76 738 80 HOH HOH . 
F 5 HOH A 77 739 81 HOH HOH . 
F 5 HOH A 78 740 82 HOH HOH . 
F 5 HOH A 79 741 83 HOH HOH . 
F 5 HOH A 80 742 84 HOH HOH . 
F 5 HOH A 81 743 85 HOH HOH . 
F 5 HOH A 82 744 86 HOH HOH . 
F 5 HOH A 83 745 87 HOH HOH . 
F 5 HOH A 84 746 88 HOH HOH . 
F 5 HOH A 85 747 89 HOH HOH . 
F 5 HOH A 86 748 90 HOH HOH . 
F 5 HOH A 87 749 91 HOH HOH . 
F 5 HOH A 88 750 92 HOH HOH . 
F 5 HOH A 89 751 93 HOH HOH . 
F 5 HOH A 90 752 95 HOH HOH . 
F 5 HOH A 91 753 96 HOH HOH . 
F 5 HOH A 92 754 97 HOH HOH . 
F 5 HOH A 93 755 98 HOH HOH . 
F 5 HOH A 94 756 99 HOH HOH . 
F 5 HOH A 95 757 100 HOH HOH . 
F 5 HOH A 96 758 101 HOH HOH . 
F 5 HOH A 97 759 102 HOH HOH . 
F 5 HOH A 98 760 103 HOH HOH . 
F 5 HOH A 99 761 104 HOH HOH . 
F 5 HOH A 100 762 106 HOH HOH . 
F 5 HOH A 101 763 107 HOH HOH . 
F 5 HOH A 102 764 108 HOH HOH . 
F 5 HOH A 103 765 109 HOH HOH . 
F 5 HOH A 104 766 110 HOH HOH . 
F 5 HOH A 105 767 113 HOH HOH . 
F 5 HOH A 106 768 114 HOH HOH . 
F 5 HOH A 107 769 115 HOH HOH . 
F 5 HOH A 108 770 116 HOH HOH . 
F 5 HOH A 109 771 117 HOH HOH . 
F 5 HOH A 110 772 118 HOH HOH . 
F 5 HOH A 111 773 119 HOH HOH . 
F 5 HOH A 112 774 120 HOH HOH . 
F 5 HOH A 113 775 121 HOH HOH . 
F 5 HOH A 114 776 122 HOH HOH . 
F 5 HOH A 115 777 123 HOH HOH . 
F 5 HOH A 116 778 124 HOH HOH . 
F 5 HOH A 117 779 125 HOH HOH . 
F 5 HOH A 118 780 126 HOH HOH . 
F 5 HOH A 119 781 127 HOH HOH . 
F 5 HOH A 120 782 128 HOH HOH . 
F 5 HOH A 121 783 129 HOH HOH . 
F 5 HOH A 122 784 130 HOH HOH . 
F 5 HOH A 123 785 131 HOH HOH . 
F 5 HOH A 124 786 132 HOH HOH . 
F 5 HOH A 125 787 133 HOH HOH . 
F 5 HOH A 126 788 135 HOH HOH . 
F 5 HOH A 127 789 136 HOH HOH . 
F 5 HOH A 128 790 137 HOH HOH . 
F 5 HOH A 129 791 138 HOH HOH . 
F 5 HOH A 130 792 139 HOH HOH . 
F 5 HOH A 131 793 140 HOH HOH . 
F 5 HOH A 132 794 141 HOH HOH . 
F 5 HOH A 133 795 142 HOH HOH . 
F 5 HOH A 134 796 144 HOH HOH . 
F 5 HOH A 135 797 145 HOH HOH . 
F 5 HOH A 136 798 146 HOH HOH . 
F 5 HOH A 137 799 148 HOH HOH . 
F 5 HOH A 138 800 149 HOH HOH . 
F 5 HOH A 139 801 150 HOH HOH . 
F 5 HOH A 140 802 151 HOH HOH . 
F 5 HOH A 141 803 152 HOH HOH . 
F 5 HOH A 142 804 153 HOH HOH . 
F 5 HOH A 143 805 154 HOH HOH . 
F 5 HOH A 144 806 155 HOH HOH . 
F 5 HOH A 145 807 156 HOH HOH . 
F 5 HOH A 146 808 157 HOH HOH . 
F 5 HOH A 147 809 158 HOH HOH . 
F 5 HOH A 148 810 159 HOH HOH . 
F 5 HOH A 149 811 160 HOH HOH . 
F 5 HOH A 150 812 161 HOH HOH . 
F 5 HOH A 151 813 162 HOH HOH . 
F 5 HOH A 152 814 163 HOH HOH . 
F 5 HOH A 153 815 164 HOH HOH . 
F 5 HOH A 154 816 165 HOH HOH . 
F 5 HOH A 155 817 166 HOH HOH . 
F 5 HOH A 156 818 167 HOH HOH . 
F 5 HOH A 157 819 168 HOH HOH . 
F 5 HOH A 158 820 169 HOH HOH . 
F 5 HOH A 159 821 170 HOH HOH . 
F 5 HOH A 160 822 171 HOH HOH . 
F 5 HOH A 161 823 172 HOH HOH . 
F 5 HOH A 162 824 173 HOH HOH . 
F 5 HOH A 163 825 174 HOH HOH . 
F 5 HOH A 164 826 175 HOH HOH . 
F 5 HOH A 165 827 176 HOH HOH . 
F 5 HOH A 166 828 177 HOH HOH . 
F 5 HOH A 167 829 178 HOH HOH . 
F 5 HOH A 168 830 179 HOH HOH . 
F 5 HOH A 169 831 180 HOH HOH . 
F 5 HOH A 170 832 181 HOH HOH . 
F 5 HOH A 171 833 183 HOH HOH . 
F 5 HOH A 172 834 184 HOH HOH . 
F 5 HOH A 173 835 185 HOH HOH . 
F 5 HOH A 174 836 186 HOH HOH . 
F 5 HOH A 175 837 187 HOH HOH . 
F 5 HOH A 176 838 188 HOH HOH . 
F 5 HOH A 177 839 189 HOH HOH . 
F 5 HOH A 178 840 190 HOH HOH . 
F 5 HOH A 179 841 191 HOH HOH . 
F 5 HOH A 180 842 192 HOH HOH . 
F 5 HOH A 181 843 193 HOH HOH . 
F 5 HOH A 182 844 194 HOH HOH . 
F 5 HOH A 183 845 195 HOH HOH . 
F 5 HOH A 184 846 196 HOH HOH . 
F 5 HOH A 185 847 197 HOH HOH . 
F 5 HOH A 186 848 198 HOH HOH . 
F 5 HOH A 187 849 199 HOH HOH . 
F 5 HOH A 188 850 201 HOH HOH . 
F 5 HOH A 189 851 202 HOH HOH . 
F 5 HOH A 190 852 203 HOH HOH . 
F 5 HOH A 191 853 204 HOH HOH . 
G 5 HOH B 1 36 36 HOH HOH . 
G 5 HOH B 2 60 60 HOH HOH . 
G 5 HOH B 3 65 65 HOH HOH . 
G 5 HOH B 4 94 94 HOH HOH . 
G 5 HOH B 5 105 105 HOH HOH . 
G 5 HOH B 6 111 111 HOH HOH . 
G 5 HOH B 7 112 112 HOH HOH . 
G 5 HOH B 8 134 134 HOH HOH . 
G 5 HOH B 9 143 143 HOH HOH . 
G 5 HOH B 10 147 147 HOH HOH . 
G 5 HOH B 11 182 182 HOH HOH . 
G 5 HOH B 12 200 200 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 . . . D 4 -2.871 -8.098 5.673 1 30.6 ? PB ADP 662 A 1 
HETATM 2 O O1B ADP . . . D 4 -1.852 -8.188 6.793 1 30.06 ? O1B ADP 662 A 1 
HETATM 3 O O2B ADP . . . D 4 -4.28 -7.637 6.068 1 27.37 ? O2B ADP 662 A 1 
HETATM 4 O O3B ADP . . . D 4 -2.792 -9.356 4.852 1 28.25 ? O3B ADP 662 A 1 
HETATM 5 P PA ADP . . . D 4 -2.313 -5.354 4.94 1 27.65 ? PA ADP 662 A 1 
HETATM 6 O O1A ADP . . . D 4 -3.747 -4.957 5.14 1 31.75 ? O1A ADP 662 A 1 
HETATM 7 O O2A ADP . . . D 4 -1.284 -5.037 5.985 1 28.92 ? O2A ADP 662 A 1 
HETATM 8 O O3A ADP . . . D 4 -2.366 -6.946 4.644 1 29.79 ? O3A ADP 662 A 1 
HETATM 9 O O5' ADP . . . D 4 -1.896 -4.733 3.509 1 29.48 ? O5' ADP 662 A 1 
HETATM 10 C C5' ADP . . . D 4 -0.617 -4.245 3.141 1 27.64 ? C5' ADP 662 A 1 
HETATM 11 C C4' ADP . . . D 4 -0.765 -2.777 2.774 1 27.53 ? C4' ADP 662 A 1 
HETATM 12 O O4' ADP . . . D 4 -1.166 -2.609 1.406 1 27.9 ? O4' ADP 662 A 1 
HETATM 13 C C3' ADP . . . D 4 -1.833 -2.085 3.604 1 26.76 ? C3' ADP 662 A 1 
HETATM 14 O O3' ADP . . . D 4 -1.366 -0.755 3.769 1 28.95 ? O3' ADP 662 A 1 
HETATM 15 C C2' ADP . . . D 4 -3.062 -2.129 2.705 1 26.87 ? C2' ADP 662 A 1 
HETATM 16 O O2' ADP . . . D 4 -4.055 -1.163 3.056 1 27.71 ? O2' ADP 662 A 1 
HETATM 17 C C1' ADP . . . D 4 -2.456 -1.949 1.306 1 25.57 ? C1' ADP 662 A 1 
HETATM 18 N N9 ADP . . . D 4 -3.228 -2.551 0.168 1 23.62 ? N9 ADP 662 A 1 
HETATM 19 C C8 ADP . . . D 4 -4.07 -3.612 0.177 1 23.58 ? C8 ADP 662 A 1 
HETATM 20 N N7 ADP . . . D 4 -4.566 -3.877 -1.065 1 23.18 ? N7 ADP 662 A 1 
HETATM 21 C C5 ADP . . . D 4 -4.021 -2.981 -1.907 1 23.16 ? C5 ADP 662 A 1 
HETATM 22 C C6 ADP . . . D 4 -4.099 -2.682 -3.359 1 23.18 ? C6 ADP 662 A 1 
HETATM 23 N N6 ADP . . . D 4 -4.877 -3.405 -4.191 1 23.13 ? N6 ADP 662 A 1 
HETATM 24 N N1 ADP . . . D 4 -3.386 -1.621 -3.827 1 24.53 ? N1 ADP 662 A 1 
HETATM 25 C C2 ADP . . . D 4 -2.593 -0.87 -3.022 1 25.24 ? C2 ADP 662 A 1 
HETATM 26 N N3 ADP . . . D 4 -2.473 -1.075 -1.685 1 25.88 ? N3 ADP 662 A 1 
HETATM 27 C C4 ADP . . . D 4 -3.142 -2.111 -1.085 1 24.08 ? C4 ADP 662 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#