data_3J8I # _model_server_result.job_id 6qIK7I2Vsgf32Mivve7nEQ _model_server_result.datetime_utc '2024-11-17 10:20:59' _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 3j8i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 3J8I # _exptl.entry_id 3J8I _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 3J8I _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J8I _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 2 F N N ? 2 H N N ? 2 J N N ? 2 L N N ? 2 N 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 F O1B ADP . D ADP 401 1_555 G MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc2 H O1B ADP . E ADP 401 1_555 I MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc3 J O1B ADP . F ADP 401 1_555 K MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc4 L O1B ADP . G ADP 401 1_555 M MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc5 N O1B ADP . H ADP 401 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? # _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 3J8I _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 F 2 ADP D 1 401 376 ADP ADP . G 3 MG D 1 402 377 MG MG . H 2 ADP E 1 401 376 ADP ADP . I 3 MG E 1 402 377 MG MG . J 2 ADP F 1 401 376 ADP ADP . K 3 MG F 1 402 377 MG MG . L 2 ADP G 1 401 376 ADP ADP . M 3 MG G 1 402 377 MG MG . N 2 ADP H 1 401 376 ADP ADP . O 3 MG H 1 402 377 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 . . . N 2 -15.378 8.291 -62.901 1 96.31 ? PB ADP 401 H 1 HETATM 2 O O1B ADP . . . N 2 -16.43 8.655 -63.884 1 98.18 ? O1B ADP 401 H 1 HETATM 3 O O2B ADP . . . N 2 -16.008 7.464 -61.676 1 91.16 ? O2B ADP 401 H 1 HETATM 4 O O3B ADP . . . N 2 -14.323 7.499 -63.604 1 86.37 ? O3B ADP 401 H 1 HETATM 5 P PA ADP . . . N 2 -13.783 10.61 -62.948 1 116.31 ? PA ADP 401 H 1 HETATM 6 O O1A ADP . . . N 2 -13.388 10.138 -64.284 1 118.99 ? O1A ADP 401 H 1 HETATM 7 O O2A ADP . . . N 2 -14.424 11.92 -63.064 1 127.35 ? O2A ADP 401 H 1 HETATM 8 O O3A ADP . . . N 2 -14.757 9.595 -62.315 1 83.18 ? O3A ADP 401 H 1 HETATM 9 O O5' ADP . . . N 2 -12.53 10.788 -61.997 1 119.26 ? O5' ADP 401 H 1 HETATM 10 C C5' ADP . . . N 2 -12.26 10.202 -60.737 1 93.76 ? C5' ADP 401 H 1 HETATM 11 C C4' ADP . . . N 2 -10.839 10.753 -60.346 1 119.54 ? C4' ADP 401 H 1 HETATM 12 O O4' ADP . . . N 2 -10.694 12.158 -60.666 1 95.72 ? O4' ADP 401 H 1 HETATM 13 C C3' ADP . . . N 2 -10.487 10.651 -58.838 1 118.7 ? C3' ADP 401 H 1 HETATM 14 O O3' ADP . . . N 2 -9.159 10.133 -58.584 1 148.48 ? O3' ADP 401 H 1 HETATM 15 C C2' ADP . . . N 2 -10.643 12.05 -58.292 1 90.77 ? C2' ADP 401 H 1 HETATM 16 O O2' ADP . . . N 2 -9.908 12.264 -57.079 1 47.45 ? O2' ADP 401 H 1 HETATM 17 C C1' ADP . . . N 2 -10.235 12.881 -59.494 1 66.64 ? C1' ADP 401 H 1 HETATM 18 N N9 ADP . . . N 2 -10.835 14.25 -59.491 1 79.9 ? N9 ADP 401 H 1 HETATM 19 C C8 ADP . . . N 2 -12.145 14.545 -59.704 1 83.19 ? C8 ADP 401 H 1 HETATM 20 N N7 ADP . . . N 2 -12.311 15.852 -59.622 1 67.47 ? N7 ADP 401 H 1 HETATM 21 C C5 ADP . . . N 2 -11.146 16.394 -59.36 1 91.33 ? C5 ADP 401 H 1 HETATM 22 C C6 ADP . . . N 2 -10.676 17.696 -59.17 1 115.93 ? C6 ADP 401 H 1 HETATM 23 N N6 ADP . . . N 2 -11.549 18.696 -59.23 1 168.63 ? N6 ADP 401 H 1 HETATM 24 N N1 ADP . . . N 2 -9.325 17.95 -58.906 1 75.18 ? N1 ADP 401 H 1 HETATM 25 C C2 ADP . . . N 2 -8.422 16.954 -58.833 1 14.34 ? C2 ADP 401 H 1 HETATM 26 N N3 ADP . . . N 2 -8.871 15.681 -59.018 1 58.33 ? N3 ADP 401 H 1 HETATM 27 C C4 ADP . . . N 2 -10.191 15.368 -59.287 1 80.75 ? C4 ADP 401 H 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #