data_6ZY9 # _model_server_result.job_id lhFIVjFrbhkdmkuSEzEyAg _model_server_result.datetime_utc '2024-11-04 23:01:01' _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 6zy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":401}' # _entry.id 6ZY9 # _exptl.entry_id 6ZY9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 506.196 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 6ZY9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZY9 _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,P _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 ? 5 M N N ? 5 O 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 I OG1 THR 48 F THR 48 1_555 N MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc2 M O2G ANP . F ANP 401 1_555 N MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc3 J OG1 THR 48 G THR 48 1_555 P MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 6ZY9 _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 M 5 ANP F 1 401 401 ANP ANP . N 6 MG F 1 402 1 MG MG . O 5 ANP G 1 401 401 ANP ANP . P 6 MG G 1 402 2 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 PG ANP . . . M 5 138.907 125.477 173.003 1 58.25 ? PG ANP 401 F 1 HETATM 2 O O1G ANP . . . M 5 139.896 125.621 171.889 1 58.25 ? O1G ANP 401 F 1 HETATM 3 O O2G ANP . . . M 5 137.457 125.343 172.396 1 58.25 ? O2G ANP 401 F 1 HETATM 4 O O3G ANP . . . M 5 138.968 126.754 173.934 1 58.25 ? O3G ANP 401 F 1 HETATM 5 P PB ANP . . . M 5 140.651 124.335 174.833 1 58.25 ? PB ANP 401 F 1 HETATM 6 O O1B ANP . . . M 5 141.286 125.638 174.473 1 58.25 ? O1B ANP 401 F 1 HETATM 7 O O2B ANP . . . M 5 140.273 124.358 176.343 1 58.25 ? O2B ANP 401 F 1 HETATM 8 N N3B ANP . . . M 5 139.262 124.099 173.921 1 58.25 ? N3B ANP 401 F 1 HETATM 9 P PA ANP . . . M 5 142.201 122.892 173.113 1 58.25 ? PA ANP 401 F 1 HETATM 10 O O1A ANP . . . M 5 141.112 122.942 172.112 1 58.25 ? O1A ANP 401 F 1 HETATM 11 O O2A ANP . . . M 5 142.923 121.542 173.171 1 58.25 ? O2A ANP 401 F 1 HETATM 12 O O3A ANP . . . M 5 141.653 123.17 174.577 1 58.25 ? O3A ANP 401 F 1 HETATM 13 O O5' ANP . . . M 5 143.215 124.066 172.802 1 58.25 ? O5' ANP 401 F 1 HETATM 14 C C5' ANP . . . M 5 144.63 123.804 172.685 1 58.25 ? C5' ANP 401 F 1 HETATM 15 C C4' ANP . . . M 5 145.27 124.834 171.786 1 58.25 ? C4' ANP 401 F 1 HETATM 16 O O4' ANP . . . M 5 145.706 124.203 170.56 1 58.25 ? O4' ANP 401 F 1 HETATM 17 C C3' ANP . . . M 5 144.378 126.007 171.376 1 58.25 ? C3' ANP 401 F 1 HETATM 18 O O3' ANP . . . M 5 145.1 127.232 171.413 1 58.25 ? O3' ANP 401 F 1 HETATM 19 C C2' ANP . . . M 5 143.95 125.64 169.953 1 58.25 ? C2' ANP 401 F 1 HETATM 20 O O2' ANP . . . M 5 143.698 126.794 169.16 1 58.25 ? O2' ANP 401 F 1 HETATM 21 C C1' ANP . . . M 5 145.185 124.899 169.447 1 58.25 ? C1' ANP 401 F 1 HETATM 22 N N9 ANP . . . M 5 144.905 123.934 168.392 1 58.25 ? N9 ANP 401 F 1 HETATM 23 C C8 ANP . . . M 5 144.195 122.764 168.504 1 58.25 ? C8 ANP 401 F 1 HETATM 24 N N7 ANP . . . M 5 144.1 122.088 167.386 1 58.25 ? N7 ANP 401 F 1 HETATM 25 C C5 ANP . . . M 5 144.795 122.862 166.471 1 58.25 ? C5 ANP 401 F 1 HETATM 26 C C6 ANP . . . M 5 145.067 122.699 165.099 1 58.25 ? C6 ANP 401 F 1 HETATM 27 N N6 ANP . . . M 5 144.65 121.652 164.379 1 58.25 ? N6 ANP 401 F 1 HETATM 28 N N1 ANP . . . M 5 145.791 123.661 164.481 1 58.25 ? N1 ANP 401 F 1 HETATM 29 C C2 ANP . . . M 5 146.21 124.71 165.196 1 58.25 ? C2 ANP 401 F 1 HETATM 30 N N3 ANP . . . M 5 146.016 124.971 166.491 1 58.25 ? N3 ANP 401 F 1 HETATM 31 C C4 ANP . . . M 5 145.296 124.002 167.075 1 58.25 ? C4 ANP 401 F 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #