data_5ONV # _model_server_result.job_id pkmrHDeUV28mYsACg9lYug _model_server_result.datetime_utc '2024-10-19 19:42:08' _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 5onv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 5ONV # _exptl.entry_id 5ONV _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 5ONV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ONV _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 ? 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 covale ? covale1 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 E C GLU 72 E GLU 72 1_555 E N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 E C HIC 73 E HIC 73 1_555 E N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 F O1B ADP . A ADP 401 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc2 H O1B ADP . B ADP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc3 J O1B ADP . C ADP 401 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc4 L O1B ADP . D ADP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc5 N O1B ADP . E ADP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? # _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 5ONV _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 A 1 401 376 ADP ADP . G 3 MG A 1 402 377 MG MG . H 2 ADP B 1 401 376 ADP ADP . I 3 MG B 1 402 377 MG MG . J 2 ADP C 1 401 376 ADP ADP . K 3 MG C 1 402 377 MG MG . L 2 ADP D 1 401 376 ADP ADP . M 3 MG D 1 402 377 MG MG . N 2 ADP E 1 401 376 ADP ADP . O 3 MG E 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 . . . H 2 128.809 150.153 119.361 1 56.71 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . H 2 128.352 150.522 117.965 1 55.13 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . H 2 127.629 149.835 120.24 1 56.14 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . H 2 130.038 149.237 119.303 1 61.92 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . H 2 128.34 152.754 119.965 1 55.3 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . H 2 128.399 153.22 118.521 1 57.24 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . H 2 126.985 152.461 120.587 1 55.06 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . H 2 129.283 151.491 120.025 1 54.24 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . H 2 129.159 153.8 120.825 1 57.44 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . H 2 129.612 153.53 122.14 1 57.22 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . H 2 131.095 153.913 122.261 1 56.41 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . H 2 131.324 155.266 121.881 1 56.28 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . H 2 131.627 153.765 123.674 1 51.51 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . H 2 132.984 153.302 123.725 1 57.1 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . H 2 131.473 155.153 124.185 1 50.74 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . H 2 132.364 155.46 125.231 1 59.59 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . H 2 131.69 156.045 123.006 1 53.05 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . H 2 130.749 157.134 123.145 1 54.97 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . H 2 129.43 156.979 123.157 1 57.95 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . H 2 128.803 158.16 123.314 1 58.99 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . H 2 129.753 159.083 123.403 1 57.25 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . H 2 129.761 160.532 123.584 1 61.75 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . H 2 128.617 161.236 123.707 1 65.32 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . H 2 130.957 161.134 123.627 1 59.5 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . H 2 132.107 160.454 123.509 1 53.98 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . H 2 132.21 159.112 123.339 1 52.33 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . H 2 131.055 158.4 123.282 1 53.18 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 27 #