data_3J8A # _model_server_result.job_id BxdrOyxQ2DdTopuoSTdYqA _model_server_result.datetime_utc '2024-10-12 19:26:45' _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 3j8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":402}' # _entry.id 3J8A # _exptl.entry_id 3J8A _exptl.method 'ELECTRON MICROSCOPY' # _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 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 3J8A _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J8A _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 ? 4 I N N ? 4 K N N ? 4 M N N ? 4 O N N ? 4 Q 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 C C GLU 72 A GLU 72 1_555 C N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 C C HIC 73 A HIC 73 1_555 C N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 D C GLU 72 B GLU 72 1_555 D N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 D C HIC 73 B HIC 73 1_555 D N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 E C GLU 72 C GLU 72 1_555 E N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 E C HIC 73 C HIC 73 1_555 E N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 F C GLU 72 D GLU 72 1_555 F N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 F C HIC 73 D HIC 73 1_555 F N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 G C GLU 72 E GLU 72 1_555 G N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 G C HIC 73 E HIC 73 1_555 G N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 N MG MG . D MG 401 1_555 O O1B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 H MG MG . A MG 401 1_555 I O1B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc3 L MG MG . C MG 401 1_555 M O1B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc4 F OE1 GLN 137 D GLN 137 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc5 P MG MG . E MG 401 1_555 Q O1B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc6 G OE1 GLN 137 E GLN 137 1_555 P MG MG . E MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc7 E OE1 GLN 137 C GLN 137 1_555 L MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc8 C OE1 GLN 137 A GLN 137 1_555 H MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc9 D OE1 GLN 137 B GLN 137 1_555 J MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc10 J MG MG . B MG 401 1_555 K O1B ADP . B ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? # _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 ? # _atom_sites.entry_id 3J8A _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 H 3 MG A 1 401 401 MG MG . I 4 ADP A 1 402 402 ADP ADP . J 3 MG B 1 401 401 MG MG . K 4 ADP B 1 402 402 ADP ADP . L 3 MG C 1 401 401 MG MG . M 4 ADP C 1 402 402 ADP ADP . N 3 MG D 1 401 401 MG MG . O 4 ADP D 1 402 402 ADP ADP . P 3 MG E 1 401 401 MG MG . Q 4 ADP E 1 402 402 ADP ADP . # 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 4 15.413 8.094 55.165 1 76.45 ? PB ADP 402 B 1 HETATM 2 O O1B ADP . . . K 4 16.388 8.62 54.139 1 76.6 ? O1B ADP 402 B 1 HETATM 3 O O2B ADP . . . K 4 15.247 8.965 56.386 1 68.69 ? O2B ADP 402 B 1 HETATM 4 O O3B ADP . . . K 4 14.12 7.576 54.589 1 72.66 ? O3B ADP 402 B 1 HETATM 5 P PA ADP . . . K 4 17.656 6.792 56.224 1 55.92 ? PA ADP 402 B 1 HETATM 6 O O1A ADP . . . K 4 18.557 6.641 55.02 1 52.23 ? O1A ADP 402 B 1 HETATM 7 O O2A ADP . . . K 4 17.819 7.958 57.171 1 57.69 ? O2A ADP 402 B 1 HETATM 8 O O3A ADP . . . K 4 16.125 6.769 55.729 1 57.65 ? O3A ADP 402 B 1 HETATM 9 O O5' ADP . . . K 4 17.666 5.433 57.081 1 60.83 ? O5' ADP 402 B 1 HETATM 10 C C5' ADP . . . K 4 17.434 5.489 58.485 1 61.5 ? C5' ADP 402 B 1 HETATM 11 C C4' ADP . . . K 4 16.57 4.297 58.87 1 57.57 ? C4' ADP 402 B 1 HETATM 12 O O4' ADP . . . K 4 17.275 3.09 58.586 1 63.77 ? O4' ADP 402 B 1 HETATM 13 C C3' ADP . . . K 4 16.215 4.292 60.351 1 59.14 ? C3' ADP 402 B 1 HETATM 14 O O3' ADP . . . K 4 14.797 4.408 60.502 1 61.86 ? O3' ADP 402 B 1 HETATM 15 C C2' ADP . . . K 4 16.702 2.961 60.895 1 59.09 ? C2' ADP 402 B 1 HETATM 16 O O2' ADP . . . K 4 15.642 2.244 61.536 1 59.69 ? O2' ADP 402 B 1 HETATM 17 C C1' ADP . . . K 4 17.198 2.182 59.686 1 60.45 ? C1' ADP 402 B 1 HETATM 18 N N9 ADP . . . K 4 18.539 1.595 59.943 1 62.19 ? N9 ADP 402 B 1 HETATM 19 C C8 ADP . . . K 4 19.661 2.273 60.258 1 60.81 ? C8 ADP 402 B 1 HETATM 20 N N7 ADP . . . K 4 20.705 1.42 60.42 1 60.19 ? N7 ADP 402 B 1 HETATM 21 C C5 ADP . . . K 4 20.258 0.169 60.205 1 62.87 ? C5 ADP 402 B 1 HETATM 22 C C6 ADP . . . K 4 20.832 -1.2 60.222 1 63.21 ? C6 ADP 402 B 1 HETATM 23 N N6 ADP . . . K 4 22.141 -1.419 60.499 1 69.55 ? N6 ADP 402 B 1 HETATM 24 N N1 ADP . . . K 4 20.004 -2.23 59.939 1 56.18 ? N1 ADP 402 B 1 HETATM 25 C C2 ADP . . . K 4 18.705 -2.034 59.66 1 57.71 ? C2 ADP 402 B 1 HETATM 26 N N3 ADP . . . K 4 18.117 -0.827 59.633 1 59.64 ? N3 ADP 402 B 1 HETATM 27 C C4 ADP . . . K 4 18.826 0.293 59.904 1 60.33 ? C4 ADP 402 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #