data_8H9S # _model_server_result.job_id 7U8uk_BzVSFfl-t-TE2Ekw _model_server_result.datetime_utc '2025-07-30 17:49:38' _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 8h9s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":501}' # _entry.id 8H9S # _exptl.entry_id 8H9S _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 21 _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 8H9S _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8H9S _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 28-meric _pdbx_struct_assembly.oligomeric_count 28 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA _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 ? _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 ? 21 JA N N ? 21 LA 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 D OG1 THR 176 A THR 176 1_555 EA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc2 DA O3G ATP . A ATP 601 1_555 EA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc3 DA O1B ATP . A ATP 601 1_555 EA MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc4 E OG1 THR 176 B THR 176 1_555 GA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc5 FA O3G ATP . B ATP 601 1_555 GA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc6 FA O1B ATP . B ATP 601 1_555 GA MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc7 F OG1 THR 176 C THR 176 1_555 IA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc8 HA O1G ATP . C ATP 601 1_555 IA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? metalc ? metalc9 HA O1B ATP . C ATP 601 1_555 IA MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc10 H OG1 THR 166 F THR 166 1_555 KA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc11 JA O3B ADP . F ADP 501 1_555 KA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc12 I OG1 THR 166 D THR 166 1_555 MA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc13 LA O1B ADP . D ADP 501 1_555 MA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? # _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 125 n n PB O2B ADP sing 126 n n PB O3B ADP sing 127 n n PB O3A ADP sing 128 n n O2B HOB2 ADP sing 129 n n O3B HOB3 ADP sing 130 n n PA O1A ADP doub 131 n n PA O2A ADP sing 132 n n PA O3A ADP sing 133 n n PA O5' ADP sing 134 n n O2A HOA2 ADP sing 135 n n O5' C5' ADP sing 136 n n C5' C4' ADP sing 137 n n C5' "H5'1" ADP sing 138 n n C5' "H5'2" ADP sing 139 n n C4' O4' ADP sing 140 n n C4' C3' ADP sing 141 n n C4' H4' ADP sing 142 n n O4' C1' ADP sing 143 n n C3' O3' ADP sing 144 n n C3' C2' ADP sing 145 n n C3' H3' ADP sing 146 n n O3' HO3' ADP sing 147 n n C2' O2' ADP sing 148 n n C2' C1' ADP sing 149 n n C2' H2' ADP sing 150 n n O2' HO2' ADP sing 151 n n C1' N9 ADP sing 152 n n C1' H1' ADP sing 153 n n N9 C8 ADP sing 154 n y N9 C4 ADP sing 155 n y C8 N7 ADP doub 156 n y C8 H8 ADP sing 157 n n N7 C5 ADP sing 158 n y C5 C6 ADP sing 159 n y C5 C4 ADP doub 160 n y C6 N6 ADP sing 161 n n C6 N1 ADP doub 162 n y N6 HN61 ADP sing 163 n n N6 HN62 ADP sing 164 n n N1 C2 ADP sing 165 n y C2 N3 ADP doub 166 n y C2 H2 ADP sing 167 n n N3 C4 ADP sing 168 n y # _atom_sites.entry_id 8H9S _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 CA 18 CDL K 1 301 551 CDL CDL . DA 19 ATP A 1 601 551 ATP ATP . EA 20 MG A 1 602 552 MG MG . FA 19 ATP B 1 601 551 ATP ATP . GA 20 MG B 1 602 552 MG MG . HA 19 ATP C 1 601 551 ATP ATP . IA 20 MG C 1 602 552 MG MG . JA 21 ADP F 1 501 551 ADP ADP . KA 20 MG F 1 502 552 MG MG . LA 21 ADP D 1 501 551 ADP ADP . MA 20 MG D 1 502 552 MG MG . NA 22 3PH Q 1 101 552 3PH 3PH . OA 18 CDL R 1 101 553 CDL CDL . # 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 . . . LA 21 205.084 168.235 145.963 1 24.54 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . LA 21 205.744 167.29 145.007 1 24.54 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . LA 21 203.639 167.9 146.089 1 24.54 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . LA 21 205.223 169.669 145.444 1 24.54 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . LA 21 207.308 167.485 147.672 1 24.54 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . LA 21 208.239 167.9 146.516 1 24.54 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . LA 21 207.22 165.94 147.74 1 24.54 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . LA 21 205.794 168.106 147.43 1 24.54 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . LA 21 207.914 168.083 149.113 1 24.54 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . LA 21 207.436 169.337 149.573 1 24.54 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . LA 21 208.001 169.612 150.903 1 24.54 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . LA 21 206.972 169.276 151.976 1 24.54 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . LA 21 209.16 168.757 151.151 1 24.54 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . LA 21 210.395 169.415 150.732 1 24.54 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . LA 21 209.169 168.549 152.59 1 24.54 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . LA 21 209.816 169.691 153.22 1 24.54 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . LA 21 207.758 168.514 153.001 1 24.54 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . LA 21 207.304 167.144 153.058 1 24.54 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . LA 21 206.652 166.594 152.099 1 24.54 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . LA 21 206.38 165.329 152.455 1 24.54 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . LA 21 206.901 165.127 153.692 1 24.54 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . LA 21 206.96 164.097 154.568 1 24.54 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . LA 21 206.333 162.778 154.224 1 24.54 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . LA 21 207.578 164.27 155.737 1 24.54 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . LA 21 208.143 165.454 156.053 1 24.54 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . LA 21 208.116 166.479 155.248 1 24.54 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . LA 21 207.519 166.387 154.064 1 24.54 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 66 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #