data_9GNR # _model_server_result.job_id 26Btk-pGg16GwssD1GYKcg _model_server_result.datetime_utc '2025-07-27 03:30:42' _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 9gnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":603}' # _entry.id 9GNR # _exptl.entry_id 9GNR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 96.026 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description DIAMIDOPHOSPHATE _entity.pdbx_number_of_molecules 1 _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 9GNR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GNR _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 CXM 1 A CXM 1 1_555 A N HIS 2 A HIS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 C C LEU 219 C LEU 219 1_555 C N KCX 220 C KCX 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 C C KCX 220 C KCX 220 1_555 C N ILE 221 C ILE 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 C NE2 HIS 137 C HIS 137 1_555 E NI NI . C NI 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 C NE2 HIS 139 C HIS 139 1_555 E NI NI . C NI 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc3 C OQ1 KCX 220 C KCX 220 1_555 D NI NI . C NI 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc4 C OQ2 KCX 220 C KCX 220 1_555 E NI NI . C NI 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc5 C ND1 HIS 249 C HIS 249 1_555 D NI NI . C NI 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc6 C NE2 HIS 275 C HIS 275 1_555 D NI NI . C NI 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc7 C OD1 ASP 363 C ASP 363 1_555 E NI NI . C NI 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc8 D NI NI . C NI 601 1_555 F O1 2PA . C 2PA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc9 D NI NI . C NI 601 1_555 F O3 2PA . C 2PA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc10 E NI NI . C NI 602 1_555 F N4 2PA . C 2PA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc11 E NI NI . C NI 602 1_555 F O3 2PA . C 2PA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? # _chem_comp.formula 'H5 N2 O2 P' _chem_comp.formula_weight 96.026 _chem_comp.id 2PA _chem_comp.mon_nstd_flag . _chem_comp.name DIAMIDOPHOSPHATE _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 N4 P2 2PA sing 1 n n N4 HN41 2PA sing 2 n n N4 HN42 2PA sing 3 n n N5 P2 2PA sing 4 n n N5 HN51 2PA sing 5 n n N5 HN52 2PA sing 6 n n O1 P2 2PA doub 7 n n P2 O3 2PA sing 8 n n O3 HO31 2PA sing 9 n n # _atom_sites.entry_id 9GNR _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 D 4 NI C 1 601 601 NI NI . E 4 NI C 1 602 602 NI NI . F 5 2PA C 1 603 617 2PA 2PA . # 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 N N4 2PA . . . F 5 128.118 123.122 105.119 1 64.64 ? N4 2PA 603 C 1 HETATM 2 N N5 2PA . . . F 5 128.982 124.544 107.099 1 51.74 ? N5 2PA 603 C 1 HETATM 3 O O1 2PA . . . F 5 130.203 124.607 104.684 1 66.83 ? O1 2PA 603 C 1 HETATM 4 P P2 2PA . . . F 5 128.878 124.617 105.396 1 53.73 ? P2 2PA 603 C 1 HETATM 5 O O3 2PA . . . F 5 127.938 125.726 105.063 1 74.41 ? O3 2PA 603 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 489 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 5 #