data_9HM9 # _model_server_result.job_id n7VxtqmVfgbmKFGYm_7yxw _model_server_result.datetime_utc '2025-07-03 02:00:31' _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 9hm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":401}' # _entry.id 9HM9 # _exptl.entry_id 9HM9 _exptl.method 'ELECTRON MICROSCOPY' # _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 5 _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 9HM9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9HM9 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,N,O,P _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 G N N ? 3 I N N ? 3 K N N ? 3 M N N ? 3 O 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 covale ? covale1 A C GLU 71 C GLU 72 1_555 A N HIC 72 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C HIC 72 C HIC 73 1_555 A N GLY 73 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 C C GLU 71 A GLU 72 1_555 C N HIC 72 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 C C HIC 72 A HIC 73 1_555 C N GLY 73 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 D C GLU 71 E GLU 72 1_555 D N HIC 72 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 D C HIC 72 E HIC 73 1_555 D N GLY 73 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 E C GLU 71 B GLU 72 1_555 E N HIC 72 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 E C HIC 72 B HIC 73 1_555 E N GLY 73 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 F C GLU 71 D GLU 72 1_555 F N HIC 72 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 F C HIC 72 D HIC 73 1_555 F N GLY 73 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 A NE2 GLN 136 C GLN 137 1_555 H MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc2 G O1B ADP . C ADP 401 1_555 H MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc3 G O2B ADP . C ADP 401 1_555 H MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc4 I O1B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc5 I O2B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc6 K O1B ADP . E ADP 401 1_555 L MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc7 K O2B ADP . E ADP 401 1_555 L MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc8 E NE2 GLN 136 B GLN 137 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc9 M O1B ADP . B ADP 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc10 M O2B ADP . B ADP 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc11 F NE2 GLN 136 D GLN 137 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc12 O O1B ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? # _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 9HM9 _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 G 3 ADP C 1 401 401 ADP ADP . H 4 MG C 1 402 402 MG MG . I 3 ADP A 1 401 401 ADP ADP . J 4 MG A 1 402 402 MG MG . K 3 ADP E 1 401 401 ADP ADP . L 4 MG E 1 402 402 MG MG . M 3 ADP B 1 401 401 ADP ADP . N 4 MG B 1 402 402 MG MG . O 3 ADP D 1 401 401 ADP ADP . P 4 MG D 1 402 402 MG MG . # 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 . . . K 3 144.313 168.245 131.501 1 101.02 ? PB ADP 401 E 1 HETATM 2 O O1B ADP . . . K 3 145.048 168.632 130.242 1 95.74 ? O1B ADP 401 E 1 HETATM 3 O O2B ADP . . . K 3 143.008 168.972 131.704 1 89.3 ? O2B ADP 401 E 1 HETATM 4 O O3B ADP . . . K 3 144.244 166.755 131.728 1 94.5 ? O3B ADP 401 E 1 HETATM 5 P PA ADP . . . K 3 145.38 170.363 132.97 1 83.13 ? PA ADP 401 E 1 HETATM 6 O O1A ADP . . . K 3 145.413 171.064 131.634 1 87.85 ? O1A ADP 401 E 1 HETATM 7 O O2A ADP . . . K 3 144.358 170.788 133.996 1 85.3 ? O2A ADP 401 E 1 HETATM 8 O O3A ADP . . . K 3 145.252 168.782 132.695 1 85.57 ? O3A ADP 401 E 1 HETATM 9 O O5' ADP . . . K 3 146.842 170.496 133.625 1 85.13 ? O5' ADP 401 E 1 HETATM 10 C C5' ADP . . . K 3 147.067 170.117 134.979 1 84.88 ? C5' ADP 401 E 1 HETATM 11 C C4' ADP . . . K 3 148.548 169.841 135.195 1 84.57 ? C4' ADP 401 E 1 HETATM 12 O O4' ADP . . . K 3 149.296 171.025 134.896 1 83.17 ? O4' ADP 401 E 1 HETATM 13 C C3' ADP . . . K 3 148.866 169.486 136.634 1 80.6 ? C3' ADP 401 E 1 HETATM 14 O O3' ADP . . . K 3 149.952 168.558 136.681 1 80.56 ? O3' ADP 401 E 1 HETATM 15 C C2' ADP . . . K 3 149.277 170.811 137.228 1 79.05 ? C2' ADP 401 E 1 HETATM 16 O O2' ADP . . . K 3 150.173 170.623 138.324 1 84.96 ? O2' ADP 401 E 1 HETATM 17 C C1' ADP . . . K 3 149.983 171.485 136.065 1 76.14 ? C1' ADP 401 E 1 HETATM 18 N N9 ADP . . . K 3 149.893 172.962 136.158 1 71.46 ? N9 ADP 401 E 1 HETATM 19 C C8 ADP . . . K 3 148.769 173.698 136.227 1 74.27 ? C8 ADP 401 E 1 HETATM 20 N N7 ADP . . . K 3 149.056 175.024 136.298 1 73.87 ? N7 ADP 401 E 1 HETATM 21 C C5 ADP . . . K 3 150.395 175.149 136.273 1 71.57 ? C5 ADP 401 E 1 HETATM 22 C C6 ADP . . . K 3 151.366 176.267 136.316 1 72.25 ? C6 ADP 401 E 1 HETATM 23 N N6 ADP . . . K 3 150.951 177.554 136.402 1 69.29 ? N6 ADP 401 E 1 HETATM 24 N N1 ADP . . . K 3 152.681 175.96 136.265 1 72.74 ? N1 ADP 401 E 1 HETATM 25 C C2 ADP . . . K 3 153.106 174.687 136.179 1 70.56 ? C2 ADP 401 E 1 HETATM 26 N N3 ADP . . . K 3 152.283 173.626 136.136 1 68.53 ? N3 ADP 401 E 1 HETATM 27 C C4 ADP . . . K 3 150.94 173.788 136.178 1 69.25 ? C4 ADP 401 E 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #