data_5ND7 # _model_server_result.job_id aH6DN23i8PIyutrFxCbG6A _model_server_result.datetime_utc '2025-07-07 03:49:31' _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 5nd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 5ND7 # _exptl.entry_id 5ND7 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _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,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 B ND2 ASN 101 A ASN 101 1_555 F O3G GTP . A GTP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? metalc ? metalc1 D MG MG . C MG 601 1_555 E O2G ANP . C ANP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 D MG MG . C MG 601 1_555 E O2B ANP . C ANP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc3 B OE1 GLU 71 A GLU 71 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc4 F O2G GTP . A GTP 500 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? # _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 5ND7 _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 MG C 1 601 504 MG MG . E 5 ANP C 1 602 505 ANP ANP . F 6 GTP A 1 500 500 GTP GTP . G 4 MG A 1 501 501 MG MG . H 7 GDP B 1 600 600 GDP GDP . I 8 TA1 B 1 601 601 TA1 TA1 . # 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 . . . E 5 186.937 208.129 313.299 1 7.79 ? PG ANP 602 C 1 HETATM 2 O O1G ANP . . . E 5 187.06 209.549 312.832 1 7.79 ? O1G ANP 602 C 1 HETATM 3 O O2G ANP . . . E 5 186.591 208.148 314.719 1 7.79 ? O2G ANP 602 C 1 HETATM 4 O O3G ANP . . . E 5 188.289 207.492 313.203 1 7.79 ? O3G ANP 602 C 1 HETATM 5 P PB ANP . . . E 5 184.966 206.017 313.008 1 7.79 ? PB ANP 602 C 1 HETATM 6 O O1B ANP . . . E 5 184.911 205.033 311.94 1 7.79 ? O1B ANP 602 C 1 HETATM 7 O O2B ANP . . . E 5 184.193 206.079 314.169 1 7.79 ? O2B ANP 602 C 1 HETATM 8 N N3B ANP . . . E 5 185.617 207.448 312.599 1 7.79 ? N3B ANP 602 C 1 HETATM 9 P PA ANP . . . E 5 182.114 206.656 312.988 1 7.79 ? PA ANP 602 C 1 HETATM 10 O O1A ANP . . . E 5 181.604 208.043 313.06 1 7.79 ? O1A ANP 602 C 1 HETATM 11 O O2A ANP . . . E 5 181.268 205.47 313.113 1 7.79 ? O2A ANP 602 C 1 HETATM 12 O O3A ANP . . . E 5 183.561 206.454 312.263 1 7.79 ? O3A ANP 602 C 1 HETATM 13 O O5' ANP . . . E 5 181.247 206.774 311.643 1 7.79 ? O5' ANP 602 C 1 HETATM 14 C C5' ANP . . . E 5 181.612 206.68 310.267 1 7.79 ? C5' ANP 602 C 1 HETATM 15 C C4' ANP . . . E 5 180.421 207.472 309.586 1 7.79 ? C4' ANP 602 C 1 HETATM 16 O O4' ANP . . . E 5 179.561 206.54 308.811 1 7.79 ? O4' ANP 602 C 1 HETATM 17 C C3' ANP . . . E 5 179.336 208.126 310.48 1 7.79 ? C3' ANP 602 C 1 HETATM 18 O O3' ANP . . . E 5 178.708 209.205 309.785 1 7.79 ? O3' ANP 602 C 1 HETATM 19 C C2' ANP . . . E 5 178.414 206.943 310.8 1 7.79 ? C2' ANP 602 C 1 HETATM 20 O O2' ANP . . . E 5 177.11 207.399 311.236 1 7.79 ? O2' ANP 602 C 1 HETATM 21 C C1' ANP . . . E 5 178.372 206.208 309.49 1 7.79 ? C1' ANP 602 C 1 HETATM 22 N N9 ANP . . . E 5 178.271 204.715 309.632 1 7.79 ? N9 ANP 602 C 1 HETATM 23 C C8 ANP . . . E 5 179.223 203.832 310.014 1 7.79 ? C8 ANP 602 C 1 HETATM 24 N N7 ANP . . . E 5 178.794 202.59 310.014 1 7.79 ? N7 ANP 602 C 1 HETATM 25 C C5 ANP . . . E 5 177.502 202.629 309.653 1 7.79 ? C5 ANP 602 C 1 HETATM 26 C C6 ANP . . . E 5 176.544 201.588 309.473 1 7.79 ? C6 ANP 602 C 1 HETATM 27 N N6 ANP . . . E 5 176.709 200.351 309.653 1 7.79 ? N6 ANP 602 C 1 HETATM 28 N N1 ANP . . . E 5 175.314 202.068 309.059 1 7.79 ? N1 ANP 602 C 1 HETATM 29 C C2 ANP . . . E 5 175.039 203.405 308.822 1 7.79 ? C2 ANP 602 C 1 HETATM 30 N N3 ANP . . . E 5 175.929 204.365 308.987 1 7.79 ? N3 ANP 602 C 1 HETATM 31 C C4 ANP . . . E 5 177.156 203.934 309.386 1 7.79 ? C4 ANP 602 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 1233 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #