data_7BIL # _model_server_result.job_id rwTfKPPOP325By3izZHcpQ _model_server_result.datetime_utc '2025-07-15 03:10:58' _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 7bil # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 7BIL # _exptl.entry_id 7BIL _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 2 _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 7BIL _cell.length_a 88.052 _cell.length_b 103.438 _cell.length_c 251.566 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BIL _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,E,F,G,H,I,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H 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 98 A THR 98 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc2 D O2B ADP . A ADP 1001 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc3 E MG MG . A MG 1002 1_555 K O HOH . A HOH 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc4 E MG MG . A MG 1002 1_555 K O HOH . A HOH 1140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc5 E MG MG . A MG 1002 1_555 K O HOH . A HOH 1153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc6 B OG1 THR 98 B THR 98 1_555 I MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc7 H O3B ADP . B ADP 1001 1_555 I MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc8 I MG MG . B MG 1002 1_555 L O HOH . B HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc9 I MG MG . B MG 1002 1_555 L O HOH . B HOH 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc10 I MG MG . B MG 1002 1_555 L O HOH . B HOH 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? hydrog 'DG-DT MISPAIR' hydrog1 C N2 DG 7 C DG 7 1_555 C O4 DT 9 C DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 7BIL _atom_sites.fract_transf_matrix[1][1] 0.011357 _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] 0.009668 _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] 0.003975 _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 3 ADP A 1 1001 1001 ADP ADP . E 4 MG A 1 1002 1002 MG MG . F 5 ALF A 1 1003 1003 ALF ALF . G 6 K A 1 1004 1 K K . H 3 ADP B 1 1001 1001 ADP ADP . I 4 MG B 1 1002 1002 MG MG . J 5 ALF B 1 1003 1003 ALF ALF . K 7 HOH A 1 1101 87 HOH HOH . K 7 HOH A 2 1102 15 HOH HOH . K 7 HOH A 3 1103 75 HOH HOH . K 7 HOH A 4 1104 48 HOH HOH . K 7 HOH A 5 1105 16 HOH HOH . K 7 HOH A 6 1106 67 HOH HOH . K 7 HOH A 7 1107 79 HOH HOH . K 7 HOH A 8 1108 51 HOH HOH . K 7 HOH A 9 1109 86 HOH HOH . K 7 HOH A 10 1110 9 HOH HOH . K 7 HOH A 11 1111 35 HOH HOH . K 7 HOH A 12 1112 100 HOH HOH . K 7 HOH A 13 1113 8 HOH HOH . K 7 HOH A 14 1114 66 HOH HOH . K 7 HOH A 15 1115 28 HOH HOH . K 7 HOH A 16 1116 42 HOH HOH . K 7 HOH A 17 1117 96 HOH HOH . K 7 HOH A 18 1118 21 HOH HOH . K 7 HOH A 19 1119 59 HOH HOH . K 7 HOH A 20 1120 34 HOH HOH . K 7 HOH A 21 1121 10 HOH HOH . K 7 HOH A 22 1122 13 HOH HOH . K 7 HOH A 23 1123 61 HOH HOH . K 7 HOH A 24 1124 106 HOH HOH . K 7 HOH A 25 1125 62 HOH HOH . K 7 HOH A 26 1126 12 HOH HOH . K 7 HOH A 27 1127 2 HOH HOH . K 7 HOH A 28 1128 43 HOH HOH . K 7 HOH A 29 1129 95 HOH HOH . K 7 HOH A 30 1130 99 HOH HOH . K 7 HOH A 31 1131 32 HOH HOH . K 7 HOH A 32 1132 3 HOH HOH . K 7 HOH A 33 1133 109 HOH HOH . K 7 HOH A 34 1134 55 HOH HOH . K 7 HOH A 35 1135 6 HOH HOH . K 7 HOH A 36 1136 53 HOH HOH . K 7 HOH A 37 1137 56 HOH HOH . K 7 HOH A 38 1138 105 HOH HOH . K 7 HOH A 39 1139 77 HOH HOH . K 7 HOH A 40 1140 52 HOH HOH . K 7 HOH A 41 1141 64 HOH HOH . K 7 HOH A 42 1142 102 HOH HOH . K 7 HOH A 43 1143 57 HOH HOH . K 7 HOH A 44 1144 84 HOH HOH . K 7 HOH A 45 1145 47 HOH HOH . K 7 HOH A 46 1146 54 HOH HOH . K 7 HOH A 47 1147 30 HOH HOH . K 7 HOH A 48 1148 29 HOH HOH . K 7 HOH A 49 1149 107 HOH HOH . K 7 HOH A 50 1150 17 HOH HOH . K 7 HOH A 51 1151 74 HOH HOH . K 7 HOH A 52 1152 25 HOH HOH . K 7 HOH A 53 1153 7 HOH HOH . K 7 HOH A 54 1154 36 HOH HOH . K 7 HOH A 55 1155 80 HOH HOH . K 7 HOH A 56 1156 31 HOH HOH . K 7 HOH A 57 1157 5 HOH HOH . K 7 HOH A 58 1158 37 HOH HOH . K 7 HOH A 59 1159 27 HOH HOH . K 7 HOH A 60 1160 22 HOH HOH . K 7 HOH A 61 1161 65 HOH HOH . K 7 HOH A 62 1162 41 HOH HOH . K 7 HOH A 63 1163 76 HOH HOH . K 7 HOH A 64 1164 91 HOH HOH . K 7 HOH A 65 1165 18 HOH HOH . K 7 HOH A 66 1166 45 HOH HOH . K 7 HOH A 67 1167 81 HOH HOH . K 7 HOH A 68 1168 88 HOH HOH . K 7 HOH A 69 1169 26 HOH HOH . K 7 HOH A 70 1170 71 HOH HOH . K 7 HOH A 71 1171 46 HOH HOH . K 7 HOH A 72 1172 19 HOH HOH . K 7 HOH A 73 1173 92 HOH HOH . K 7 HOH A 74 1174 85 HOH HOH . K 7 HOH A 75 1175 104 HOH HOH . K 7 HOH A 76 1176 63 HOH HOH . K 7 HOH A 77 1177 20 HOH HOH . K 7 HOH A 78 1178 93 HOH HOH . K 7 HOH A 79 1179 97 HOH HOH . K 7 HOH A 80 1180 83 HOH HOH . K 7 HOH A 81 1181 73 HOH HOH . K 7 HOH A 82 1182 72 HOH HOH . K 7 HOH A 83 1183 98 HOH HOH . K 7 HOH A 84 1184 101 HOH HOH . K 7 HOH A 85 1185 50 HOH HOH . K 7 HOH A 86 1186 110 HOH HOH . K 7 HOH A 87 1187 82 HOH HOH . L 7 HOH B 1 1101 89 HOH HOH . L 7 HOH B 2 1102 33 HOH HOH . L 7 HOH B 3 1103 70 HOH HOH . L 7 HOH B 4 1104 40 HOH HOH . L 7 HOH B 5 1105 68 HOH HOH . L 7 HOH B 6 1106 78 HOH HOH . L 7 HOH B 7 1107 1 HOH HOH . L 7 HOH B 8 1108 39 HOH HOH . L 7 HOH B 9 1109 24 HOH HOH . L 7 HOH B 10 1110 11 HOH HOH . L 7 HOH B 11 1111 90 HOH HOH . L 7 HOH B 12 1112 69 HOH HOH . L 7 HOH B 13 1113 44 HOH HOH . L 7 HOH B 14 1114 14 HOH HOH . L 7 HOH B 15 1115 4 HOH HOH . L 7 HOH B 16 1116 103 HOH HOH . L 7 HOH B 17 1117 94 HOH HOH . L 7 HOH B 18 1118 23 HOH HOH . L 7 HOH B 19 1119 49 HOH HOH . L 7 HOH B 20 1120 60 HOH HOH . L 7 HOH B 21 1121 38 HOH HOH . L 7 HOH B 22 1122 58 HOH HOH . M 7 HOH C 1 101 108 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 3 19.833 -0.664 -57.099 1 39.65 ? PB ADP 1001 A 1 HETATM 2 O O1B ADP . . . D 3 19.9 0.411 -58.113 1 34.67 ? O1B ADP 1001 A 1 HETATM 3 O O2B ADP . . . D 3 21.201 -1.123 -56.502 1 40.34 ? O2B ADP 1001 A 1 HETATM 4 O O3B ADP . . . D 3 18.791 -0.27 -56.088 1 33.51 ? O3B ADP 1001 A 1 HETATM 5 P PA ADP . . . D 3 19.778 -3.474 -58.039 1 35.32 ? PA ADP 1001 A 1 HETATM 6 O O1A ADP . . . D 3 21.122 -3.546 -58.834 1 44.22 ? O1A ADP 1001 A 1 HETATM 7 O O2A ADP . . . D 3 19.666 -4.148 -56.688 1 34.61 ? O2A ADP 1001 A 1 HETATM 8 O O3A ADP . . . D 3 19.336 -1.9 -57.942 1 31.05 ? O3A ADP 1001 A 1 HETATM 9 O O5' ADP . . . D 3 18.655 -4.032 -59.053 1 42.63 ? O5' ADP 1001 A 1 HETATM 10 C C5' ADP . . . D 3 17.276 -4.138 -58.644 1 47.2 ? C5' ADP 1001 A 1 HETATM 11 C C4' ADP . . . D 3 16.617 -5.4 -59.224 1 41.02 ? C4' ADP 1001 A 1 HETATM 12 O O4' ADP . . . D 3 16.635 -5.4 -60.666 1 38.76 ? O4' ADP 1001 A 1 HETATM 13 C C3' ADP . . . D 3 17.434 -6.614 -58.801 1 47.7 ? C3' ADP 1001 A 1 HETATM 14 O O3' ADP . . . D 3 16.522 -7.719 -58.611 1 42.65 ? O3' ADP 1001 A 1 HETATM 15 C C2' ADP . . . D 3 18.376 -6.894 -59.972 1 44.36 ? C2' ADP 1001 A 1 HETATM 16 O O2' ADP . . . D 3 18.671 -8.284 -60.138 1 40.35 ? O2' ADP 1001 A 1 HETATM 17 C C1' ADP . . . D 3 17.506 -6.473 -61.131 1 47.05 ? C1' ADP 1001 A 1 HETATM 18 N N9 ADP . . . D 3 18.344 -5.893 -62.203 1 49.27 ? N9 ADP 1001 A 1 HETATM 19 C C8 ADP . . . D 3 19.197 -4.832 -62.114 1 39.46 ? C8 ADP 1001 A 1 HETATM 20 N N7 ADP . . . D 3 19.721 -4.551 -63.338 1 40.07 ? N7 ADP 1001 A 1 HETATM 21 C C5 ADP . . . D 3 19.228 -5.454 -64.217 1 42.84 ? C5 ADP 1001 A 1 HETATM 22 C C6 ADP . . . D 3 19.345 -5.745 -65.668 1 54.96 ? C6 ADP 1001 A 1 HETATM 23 N N6 ADP . . . D 3 20.152 -5.025 -66.475 1 57.02 ? N6 ADP 1001 A 1 HETATM 24 N N1 ADP . . . D 3 18.614 -6.761 -66.18 1 63.4 ? N1 ADP 1001 A 1 HETATM 25 C C2 ADP . . . D 3 17.782 -7.505 -65.425 1 60.55 ? C2 ADP 1001 A 1 HETATM 26 N N3 ADP . . . D 3 17.61 -7.296 -64.114 1 53.9 ? N3 ADP 1001 A 1 HETATM 27 C C4 ADP . . . D 3 18.296 -6.314 -63.468 1 47.73 ? C4 ADP 1001 A 1 # _model_server_stats.io_time_ms 142 _model_server_stats.parse_time_ms 74 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 1567 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 27 #