data_7PMD # _model_server_result.job_id ENVLKuOdQyZMYRwa14ytTw _model_server_result.datetime_utc '2025-09-04 14:56:15' _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 7pmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1901}' # _entry.id 7PMD # _exptl.entry_id 7PMD _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7PMD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PMD _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 C GLU 74 C GLU 72 1_555 B N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 B C HIC 75 C HIC 73 1_555 B N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale3 C C TRP 1 H TRP 1 1_555 C N EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale4 C CD1 TRP 1 H TRP 1 1_555 C SG CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? covale ? covale5 C N TRP 1 H TRP 1 1_555 C C ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale6 C C EEP 2 H EEP 2 1_555 C N ALA 3 H ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale7 C C ALA 3 H ALA 3 1_555 C N DTH 4 H DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale8 C C DTH 4 H DTH 4 1_555 C N CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 C C CYS 5 H CYS 5 1_555 C N HYP 6 H HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 C C HYP 6 H HYP 6 1_555 C N ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? metalc ? metalc1 A OG SER 218 A SER 218 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc2 E O2G ANP . A ANP 1901 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? metalc ? metalc3 E O3G ANP . A ANP 1901 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc4 E O1B ANP . A ANP 1901 1_555 G MG MG . A MG 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc5 E O1A ANP . A ANP 1901 1_555 G MG MG . A MG 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc6 H O3B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? # _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 ? # _atom_sites.entry_id 7PMD _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 E 5 ANP A 1 1901 793 ANP ANP . F 6 MG A 1 1902 794 MG MG . G 6 MG A 1 1903 795 MG MG . H 7 ADP C 1 401 376 ADP ADP . I 6 MG C 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 PG ANP . . . E 5 182.786 178.908 175.692 1 93.13 ? PG ANP 1901 A 1 HETATM 2 O O1G ANP . . . E 5 182.537 177.983 176.835 1 93.13 ? O1G ANP 1901 A 1 HETATM 3 O O2G ANP . . . E 5 182.84 180.369 176.261 1 93.13 ? O2G ANP 1901 A 1 HETATM 4 O O3G ANP . . . E 5 181.66 178.803 174.591 1 93.13 ? O3G ANP 1901 A 1 HETATM 5 P PB ANP . . . E 5 185.389 178.954 176.214 1 93.13 ? PB ANP 1901 A 1 HETATM 6 O O1B ANP . . . E 5 186.53 179.726 175.647 1 93.13 ? O1B ANP 1901 A 1 HETATM 7 O O2B ANP . . . E 5 184.685 179.863 177.252 1 93.13 ? O2B ANP 1901 A 1 HETATM 8 N N3B ANP . . . E 5 184.292 178.567 175.021 1 93.13 ? N3B ANP 1901 A 1 HETATM 9 P PA ANP . . . E 5 187.187 176.94 176.641 1 93.13 ? PA ANP 1901 A 1 HETATM 10 O O1A ANP . . . E 5 188.13 177.759 175.855 1 93.13 ? O1A ANP 1901 A 1 HETATM 11 O O2A ANP . . . E 5 186.821 175.609 175.989 1 93.13 ? O2A ANP 1901 A 1 HETATM 12 O O3A ANP . . . E 5 185.817 177.646 176.923 1 93.13 ? O3A ANP 1901 A 1 HETATM 13 O O5' ANP . . . E 5 187.798 176.757 178.077 1 93.13 ? O5' ANP 1901 A 1 HETATM 14 C C5' ANP . . . E 5 188.061 177.92 178.874 1 93.13 ? C5' ANP 1901 A 1 HETATM 15 C C4' ANP . . . E 5 189.11 177.598 179.903 1 93.13 ? C4' ANP 1901 A 1 HETATM 16 O O4' ANP . . . E 5 188.819 176.326 180.525 1 93.13 ? O4' ANP 1901 A 1 HETATM 17 C C3' ANP . . . E 5 190.537 177.492 179.369 1 93.13 ? C3' ANP 1901 A 1 HETATM 18 O O3' ANP . . . E 5 191.468 178.037 180.294 1 93.13 ? O3' ANP 1901 A 1 HETATM 19 C C2' ANP . . . E 5 190.723 175.986 179.206 1 93.13 ? C2' ANP 1901 A 1 HETATM 20 O O2' ANP . . . E 5 192.088 175.609 179.326 1 93.13 ? O2' ANP 1901 A 1 HETATM 21 C C1' ANP . . . E 5 189.933 175.468 180.4 1 93.13 ? C1' ANP 1901 A 1 HETATM 22 N N9 ANP . . . E 5 189.451 174.105 180.249 1 93.13 ? N9 ANP 1901 A 1 HETATM 23 C C8 ANP . . . E 5 188.169 173.704 179.991 1 93.13 ? C8 ANP 1901 A 1 HETATM 24 N N7 ANP . . . E 5 188.024 172.405 179.9 1 93.13 ? N7 ANP 1901 A 1 HETATM 25 C C5 ANP . . . E 5 189.303 171.918 180.108 1 93.13 ? C5 ANP 1901 A 1 HETATM 26 C C6 ANP . . . E 5 189.825 170.614 180.136 1 93.13 ? C6 ANP 1901 A 1 HETATM 27 N N6 ANP . . . E 5 189.091 169.517 179.945 1 93.13 ? N6 ANP 1901 A 1 HETATM 28 N N1 ANP . . . E 5 191.147 170.474 180.368 1 93.13 ? N1 ANP 1901 A 1 HETATM 29 C C2 ANP . . . E 5 191.886 171.57 180.552 1 93.13 ? C2 ANP 1901 A 1 HETATM 30 N N3 ANP . . . E 5 191.505 172.848 180.55 1 93.13 ? N3 ANP 1901 A 1 HETATM 31 C C4 ANP . . . E 5 190.192 172.954 180.323 1 93.13 ? C4 ANP 1901 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #