data_3J8A # _model_server_result.job_id lkXC2khNDUBoplkNnla4Lg _model_server_result.datetime_utc '2024-10-12 19:27:07' _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":"M","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 . . . M 4 15.652 -6.293 -54.537 1 84.58 ? PB ADP 402 C 1 HETATM 2 O O1B ADP . . . M 4 14.854 -5.425 -55.478 1 70.84 ? O1B ADP 402 C 1 HETATM 3 O O2B ADP . . . M 4 15.957 -5.657 -53.201 1 61.18 ? O2B ADP 402 C 1 HETATM 4 O O3B ADP . . . M 4 16.822 -7 -55.178 1 85.18 ? O3B ADP 402 C 1 HETATM 5 P PA ADP . . . M 4 15.197 -8.813 -53.437 1 73.05 ? PA ADP 402 C 1 HETATM 6 O O1A ADP . . . M 4 15.599 -9.814 -54.496 1 54.43 ? O1A ADP 402 C 1 HETATM 7 O O2A ADP . . . M 4 16.179 -8.37 -52.374 1 64.58 ? O2A ADP 402 C 1 HETATM 8 O O3A ADP . . . M 4 14.644 -7.491 -54.17 1 67.22 ? O3A ADP 402 C 1 HETATM 9 O O5' ADP . . . M 4 13.863 -9.327 -52.699 1 68.6 ? O5' ADP 402 C 1 HETATM 10 C C5' ADP . . . M 4 13.79 -9.338 -51.275 1 64.81 ? C5' ADP 402 C 1 HETATM 11 C C4' ADP . . . M 4 12.339 -9.55 -50.869 1 62.64 ? C4' ADP 402 C 1 HETATM 12 O O4' ADP . . . M 4 11.951 -10.88 -51.208 1 66.58 ? O4' ADP 402 C 1 HETATM 13 C C3' ADP . . . M 4 12.129 -9.373 -49.373 1 68.97 ? C3' ADP 402 C 1 HETATM 14 O O3' ADP . . . M 4 11.326 -8.216 -49.128 1 63.51 ? O3' ADP 402 C 1 HETATM 15 C C2' ADP . . . M 4 11.405 -10.62 -48.902 1 72.91 ? C2' ADP 402 C 1 HETATM 16 O O2' ADP . . . M 4 10.127 -10.27 -48.361 1 69.7 ? O2' ADP 402 C 1 HETATM 17 C C1' ADP . . . M 4 11.221 -11.486 -50.138 1 69.92 ? C1' ADP 402 C 1 HETATM 18 N N9 ADP . . . M 4 11.731 -12.863 -49.905 1 70.93 ? N9 ADP 402 C 1 HETATM 19 C C8 ADP . . . M 4 13.02 -13.215 -49.728 1 70.98 ? C8 ADP 402 C 1 HETATM 20 N N7 ADP . . . M 4 13.135 -14.555 -49.544 1 68.7 ? N7 ADP 402 C 1 HETATM 21 C C5 ADP . . . M 4 11.9 -15.088 -49.605 1 66.99 ? C5 ADP 402 C 1 HETATM 22 C C6 ADP . . . M 4 11.307 -16.443 -49.488 1 63.57 ? C6 ADP 402 C 1 HETATM 23 N N6 ADP . . . M 4 12.077 -17.538 -49.267 1 68.45 ? N6 ADP 402 C 1 HETATM 24 N N1 ADP . . . M 4 9.966 -16.547 -49.613 1 62.49 ? N1 ADP 402 C 1 HETATM 25 C C2 ADP . . . M 4 9.187 -15.472 -49.83 1 62.26 ? C2 ADP 402 C 1 HETATM 26 N N3 ADP . . . M 4 9.655 -14.217 -49.945 1 61.27 ? N3 ADP 402 C 1 HETATM 27 C C4 ADP . . . M 4 10.979 -13.964 -49.834 1 66.01 ? C4 ADP 402 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 27 #