data_8RI2 # _model_server_result.job_id L-Nlc0Mvmt-1awXFJ6QX4A _model_server_result.datetime_utc '2024-10-19 03:56:06' _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 8ri2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 8RI2 # _exptl.entry_id 8RI2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 120 _cell.entry_id 8RI2 _cell.length_a 96.238 _cell.length_b 96.238 _cell.length_c 267.973 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RI2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 # _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 57 n n PB O2B ADP sing 58 n n PB O3B ADP sing 59 n n PB O3A ADP sing 60 n n O2B HOB2 ADP sing 61 n n O3B HOB3 ADP sing 62 n n PA O1A ADP doub 63 n n PA O2A ADP sing 64 n n PA O3A ADP sing 65 n n PA O5' ADP sing 66 n n O2A HOA2 ADP sing 67 n n O5' C5' ADP sing 68 n n C5' C4' ADP sing 69 n n C5' "H5'1" ADP sing 70 n n C5' "H5'2" ADP sing 71 n n C4' O4' ADP sing 72 n n C4' C3' ADP sing 73 n n C4' H4' ADP sing 74 n n O4' C1' ADP sing 75 n n C3' O3' ADP sing 76 n n C3' C2' ADP sing 77 n n C3' H3' ADP sing 78 n n O3' HO3' ADP sing 79 n n C2' O2' ADP sing 80 n n C2' C1' ADP sing 81 n n C2' H2' ADP sing 82 n n O2' HO2' ADP sing 83 n n C1' N9 ADP sing 84 n n C1' H1' ADP sing 85 n n N9 C8 ADP sing 86 n y N9 C4 ADP sing 87 n y C8 N7 ADP doub 88 n y C8 H8 ADP sing 89 n n N7 C5 ADP sing 90 n y C5 C6 ADP sing 91 n y C5 C4 ADP doub 92 n y C6 N6 ADP sing 93 n n C6 N1 ADP doub 94 n y N6 HN61 ADP sing 95 n n N6 HN62 ADP sing 96 n n N1 C2 ADP sing 97 n y C2 N3 ADP doub 98 n y C2 H2 ADP sing 99 n n N3 C4 ADP sing 100 n y # _atom_sites.entry_id 8RI2 _atom_sites.fract_transf_matrix[1][1] 0.010391 _atom_sites.fract_transf_matrix[1][2] 0.005999 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011998 _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] 0.003732 _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 A1H02 A 1 701 1 A1H02 LI1 . C 3 ADP A 1 702 1 ADP ADP . D 4 HOH A 1 801 11 HOH HOH . D 4 HOH A 2 802 5 HOH HOH . D 4 HOH A 3 803 45 HOH HOH . D 4 HOH A 4 804 47 HOH HOH . D 4 HOH A 5 805 21 HOH HOH . D 4 HOH A 6 806 83 HOH HOH . D 4 HOH A 7 807 60 HOH HOH . D 4 HOH A 8 808 52 HOH HOH . D 4 HOH A 9 809 12 HOH HOH . D 4 HOH A 10 810 1 HOH HOH . D 4 HOH A 11 811 99 HOH HOH . D 4 HOH A 12 812 6 HOH HOH . D 4 HOH A 13 813 33 HOH HOH . D 4 HOH A 14 814 91 HOH HOH . D 4 HOH A 15 815 73 HOH HOH . D 4 HOH A 16 816 26 HOH HOH . D 4 HOH A 17 817 76 HOH HOH . D 4 HOH A 18 818 32 HOH HOH . D 4 HOH A 19 819 50 HOH HOH . D 4 HOH A 20 820 40 HOH HOH . D 4 HOH A 21 821 8 HOH HOH . D 4 HOH A 22 822 70 HOH HOH . D 4 HOH A 23 823 61 HOH HOH . D 4 HOH A 24 824 24 HOH HOH . D 4 HOH A 25 825 49 HOH HOH . D 4 HOH A 26 826 4 HOH HOH . D 4 HOH A 27 827 53 HOH HOH . D 4 HOH A 28 828 48 HOH HOH . D 4 HOH A 29 829 13 HOH HOH . D 4 HOH A 30 830 30 HOH HOH . D 4 HOH A 31 831 100 HOH HOH . D 4 HOH A 32 832 7 HOH HOH . D 4 HOH A 33 833 104 HOH HOH . D 4 HOH A 34 834 72 HOH HOH . D 4 HOH A 35 835 56 HOH HOH . D 4 HOH A 36 836 17 HOH HOH . D 4 HOH A 37 837 89 HOH HOH . D 4 HOH A 38 838 69 HOH HOH . D 4 HOH A 39 839 19 HOH HOH . D 4 HOH A 40 840 9 HOH HOH . D 4 HOH A 41 841 15 HOH HOH . D 4 HOH A 42 842 88 HOH HOH . D 4 HOH A 43 843 39 HOH HOH . D 4 HOH A 44 844 81 HOH HOH . D 4 HOH A 45 845 75 HOH HOH . D 4 HOH A 46 846 62 HOH HOH . D 4 HOH A 47 847 51 HOH HOH . D 4 HOH A 48 848 86 HOH HOH . D 4 HOH A 49 849 64 HOH HOH . D 4 HOH A 50 850 115 HOH HOH . D 4 HOH A 51 851 16 HOH HOH . D 4 HOH A 52 852 109 HOH HOH . D 4 HOH A 53 853 79 HOH HOH . D 4 HOH A 54 854 37 HOH HOH . D 4 HOH A 55 855 20 HOH HOH . D 4 HOH A 56 856 27 HOH HOH . D 4 HOH A 57 857 84 HOH HOH . D 4 HOH A 58 858 55 HOH HOH . D 4 HOH A 59 859 102 HOH HOH . D 4 HOH A 60 860 29 HOH HOH . D 4 HOH A 61 861 34 HOH HOH . D 4 HOH A 62 862 54 HOH HOH . D 4 HOH A 63 863 78 HOH HOH . D 4 HOH A 64 864 58 HOH HOH . D 4 HOH A 65 865 63 HOH HOH . D 4 HOH A 66 866 74 HOH HOH . D 4 HOH A 67 867 43 HOH HOH . D 4 HOH A 68 868 46 HOH HOH . D 4 HOH A 69 869 66 HOH HOH . D 4 HOH A 70 870 3 HOH HOH . D 4 HOH A 71 871 28 HOH HOH . D 4 HOH A 72 872 18 HOH HOH . D 4 HOH A 73 873 31 HOH HOH . D 4 HOH A 74 874 25 HOH HOH . D 4 HOH A 75 875 87 HOH HOH . D 4 HOH A 76 876 35 HOH HOH . D 4 HOH A 77 877 85 HOH HOH . D 4 HOH A 78 878 68 HOH HOH . D 4 HOH A 79 879 94 HOH HOH . D 4 HOH A 80 880 71 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 3 16.458 34.88 139.129 1 61.51 ? PB ADP 702 A 1 HETATM 2 O O1B ADP . . . C 3 15.823 35.226 140.457 1 61.62 ? O1B ADP 702 A 1 HETATM 3 O O2B ADP . . . C 3 15.532 34.101 138.214 1 61.18 ? O2B ADP 702 A 1 HETATM 4 O O3B ADP . . . C 3 17.083 36.077 138.441 1 61.72 ? O3B ADP 702 A 1 HETATM 5 P PA ADP . . . C 3 18.47 33.678 140.912 1 62.09 ? PA ADP 702 A 1 HETATM 6 O O1A ADP . . . C 3 18.822 34.994 141.48 1 62.25 ? O1A ADP 702 A 1 HETATM 7 O O2A ADP . . . C 3 17.681 32.721 141.724 1 62.08 ? O2A ADP 702 A 1 HETATM 8 O O3A ADP . . . C 3 17.692 33.951 139.545 1 61.55 ? O3A ADP 702 A 1 HETATM 9 O O5' ADP . . . C 3 19.844 32.991 140.447 1 62.79 ? O5' ADP 702 A 1 HETATM 10 C C5' ADP . . . C 3 19.952 31.573 140.16 1 62.84 ? C5' ADP 702 A 1 HETATM 11 C C4' ADP . . . C 3 21.356 31.092 140.444 1 62.81 ? C4' ADP 702 A 1 HETATM 12 O O4' ADP . . . C 3 22.295 32.029 139.879 1 62.77 ? O4' ADP 702 A 1 HETATM 13 C C3' ADP . . . C 3 21.747 31 141.916 1 62.99 ? C3' ADP 702 A 1 HETATM 14 O O3' ADP . . . C 3 21.367 29.755 142.499 1 63.18 ? O3' ADP 702 A 1 HETATM 15 C C2' ADP . . . C 3 23.272 31.145 141.863 1 63.09 ? C2' ADP 702 A 1 HETATM 16 O O2' ADP . . . C 3 23.969 29.913 141.672 1 63.39 ? O2' ADP 702 A 1 HETATM 17 C C1' ADP . . . C 3 23.46 32.102 140.679 1 62.83 ? C1' ADP 702 A 1 HETATM 18 N N9 ADP . . . C 3 23.665 33.49 141.069 1 62.59 ? N9 ADP 702 A 1 HETATM 19 C C8 ADP . . . C 3 22.836 34.554 140.823 1 62.44 ? C8 ADP 702 A 1 HETATM 20 N N7 ADP . . . C 3 23.325 35.71 141.198 1 62.3 ? N7 ADP 702 A 1 HETATM 21 C C5 ADP . . . C 3 24.565 35.384 141.729 1 62.09 ? C5 ADP 702 A 1 HETATM 22 C C6 ADP . . . C 3 25.596 36.169 142.277 1 61.68 ? C6 ADP 702 A 1 HETATM 23 N N6 ADP . . . C 3 25.538 37.495 142.372 1 61.52 ? N6 ADP 702 A 1 HETATM 24 N N1 ADP . . . C 3 26.712 35.536 142.702 1 61.53 ? N1 ADP 702 A 1 HETATM 25 C C2 ADP . . . C 3 26.782 34.207 142.576 1 61.7 ? C2 ADP 702 A 1 HETATM 26 N N3 ADP . . . C 3 25.876 33.363 142.074 1 61.94 ? N3 ADP 702 A 1 HETATM 27 C C4 ADP . . . C 3 24.785 34.02 141.66 1 62.27 ? C4 ADP 702 A 1 HETATM 28 H "H5'1" ADP . . . C 3 19.668 31.329 139.133 0 62.84 ? "H5'1" ADP 702 A 1 HETATM 29 H "H5'2" ADP . . . C 3 19.254 31.023 140.794 0 62.84 ? "H5'2" ADP 702 A 1 HETATM 30 H H4' ADP . . . C 3 21.515 30.133 139.942 0 62.81 ? H4' ADP 702 A 1 HETATM 31 H H3' ADP . . . C 3 21.335 31.834 142.492 0 62.99 ? H3' ADP 702 A 1 HETATM 32 H HO3' ADP . . . C 3 20.406 29.829 142.625 0 63.18 ? HO3' ADP 702 A 1 HETATM 33 H H2' ADP . . . C 3 23.66 31.559 142.799 0 63.09 ? H2' ADP 702 A 1 HETATM 34 H HO2' ADP . . . C 3 23.709 29.375 142.441 0 63.39 ? HO2' ADP 702 A 1 HETATM 35 H H1' ADP . . . C 3 24.301 31.85 140.023 0 62.83 ? H1' ADP 702 A 1 HETATM 36 H H8 ADP . . . C 3 21.865 34.436 140.367 0 62.44 ? H8 ADP 702 A 1 HETATM 37 H HN61 ADP . . . C 3 26.327 37.99 142.782 0 61.52 ? HN61 ADP 702 A 1 HETATM 38 H HN62 ADP . . . C 3 24.701 37.961 142.028 0 61.52 ? HN62 ADP 702 A 1 HETATM 39 H H2 ADP . . . C 3 27.699 33.75 142.93 0 61.7 ? H2 ADP 702 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 39 #