data_3ZRY # _model_server_result.job_id xNr3mYLG2-j0zPnhypKLeA _model_server_result.datetime_utc '2024-11-15 05:30:48' _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 3zry # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":600}' # _entry.id 3ZRY # _exptl.entry_id 3ZRY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 93.92 _cell.angle_gamma 90 _cell.entry_id 3ZRY _cell.length_a 107.69 _cell.length_b 174.91 _cell.length_c 164.26 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZRY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA nonameric 9 author_and_software_defined_assembly 1 PISA decameric 10 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,T,U,V,W,X,Y,Z,AA,BA,CA 1 1 J,K,L,M,N,O,P,Q,R,S 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 T N N ? 7 V N N ? 7 X N N ? 7 Z N N ? 7 BA 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 A OG1 THR 178 A THR 178 1_555 U MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc2 T O1G ANP . A ANP 600 1_555 U MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc3 T O1B ANP . A ANP 600 1_555 U MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc4 B OG1 THR 178 B THR 178 1_555 W MG MG . B MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc5 V O1G ANP . B ANP 600 1_555 W MG MG . B MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc6 C OG1 THR 178 C THR 178 1_555 Y MG MG . C MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc7 X O1G ANP . C ANP 600 1_555 Y MG MG . C MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc8 D OG1 THR 164 D THR 164 1_555 AA MG MG . D MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc9 D OE2 GLU 193 D GLU 193 1_555 AA MG MG . D MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc10 Z O1G ANP . D ANP 600 1_555 AA MG MG . D MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc11 Z O1B ANP . D ANP 600 1_555 AA MG MG . D MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc12 F OG1 THR 164 F THR 164 1_555 CA MG MG . F MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc13 F OE1 GLU 189 F GLU 189 1_555 CA MG MG . F MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc14 F OD1 ASP 256 F ASP 256 1_555 CA MG MG . F MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc15 BA O1G ANP . F ANP 600 1_555 CA MG MG . F MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? # _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 3ZRY _atom_sites.fract_transf_matrix[1][1] 0.009286 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000636 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005717 _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] 0.006102 _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 T 7 ANP A 1 600 600 ANP ANP . U 8 MG A 1 700 700 MG MG . V 7 ANP B 1 600 600 ANP ANP . W 8 MG B 1 700 700 MG MG . X 7 ANP C 1 600 600 ANP ANP . Y 8 MG C 1 700 700 MG MG . Z 7 ANP D 1 600 600 ANP ANP . AA 8 MG D 1 700 700 MG MG . BA 7 ANP F 1 600 600 ANP ANP . CA 8 MG F 1 700 700 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 . . . V 7 3.844 11.039 15.972 1 216.19 ? PG ANP 600 B 1 HETATM 2 O O1G ANP . . . V 7 4.817 12.167 15.513 1 213.66 ? O1G ANP 600 B 1 HETATM 3 O O2G ANP . . . V 7 2.93 10.665 14.853 1 218.9 ? O2G ANP 600 B 1 HETATM 4 O O3G ANP . . . V 7 4.701 9.826 16.426 1 216.29 ? O3G ANP 600 B 1 HETATM 5 P PB ANP . . . V 7 3.815 12.287 18.378 1 195.77 ? PB ANP 600 B 1 HETATM 6 O O1B ANP . . . V 7 4.365 13.375 17.602 1 194.78 ? O1B ANP 600 B 1 HETATM 7 O O2B ANP . . . V 7 4.757 11.443 19.296 1 196.82 ? O2B ANP 600 B 1 HETATM 8 N N3B ANP . . . V 7 2.963 11.577 17.276 1 207.56 ? N3B ANP 600 B 1 HETATM 9 P PA ANP . . . V 7 2.248 14.282 18.414 1 196.26 ? PA ANP 600 B 1 HETATM 10 O O1A ANP . . . V 7 1.87 13.795 17.091 1 190.71 ? O1A ANP 600 B 1 HETATM 11 O O2A ANP . . . V 7 3.164 15.541 18.53 1 197.19 ? O2A ANP 600 B 1 HETATM 12 O O3A ANP . . . V 7 2.7 13.017 18.967 1 196.77 ? O3A ANP 600 B 1 HETATM 13 O O5' ANP . . . V 7 0.883 14.322 18.968 1 198.16 ? O5' ANP 600 B 1 HETATM 14 C C5' ANP . . . V 7 -0.115 13.436 18.539 1 202.82 ? C5' ANP 600 B 1 HETATM 15 C C4' ANP . . . V 7 -1.494 13.817 19.063 1 210.04 ? C4' ANP 600 B 1 HETATM 16 O O4' ANP . . . V 7 -1.451 14.141 20.447 1 214.47 ? O4' ANP 600 B 1 HETATM 17 C C3' ANP . . . V 7 -2.098 14.975 18.326 1 212.73 ? C3' ANP 600 B 1 HETATM 18 O O3' ANP . . . V 7 -1.463 15.2 17.118 1 214.61 ? O3' ANP 600 B 1 HETATM 19 C C2' ANP . . . V 7 -1.948 16.121 19.248 1 216.09 ? C2' ANP 600 B 1 HETATM 20 O O2' ANP . . . V 7 -3.181 16.616 19.619 1 220.08 ? O2' ANP 600 B 1 HETATM 21 C C1' ANP . . . V 7 -1.146 15.519 20.364 1 218.27 ? C1' ANP 600 B 1 HETATM 22 N N9 ANP . . . V 7 -1.031 16.195 21.674 1 219.83 ? N9 ANP 600 B 1 HETATM 23 C C8 ANP . . . V 7 0.181 16.371 22.212 1 218.25 ? C8 ANP 600 B 1 HETATM 24 N N7 ANP . . . V 7 0.099 16.983 23.383 1 218.82 ? N7 ANP 600 B 1 HETATM 25 C C5 ANP . . . V 7 -1.182 17.228 23.655 1 222.15 ? C5 ANP 600 B 1 HETATM 26 C C6 ANP . . . V 7 -1.81 17.839 24.736 1 224.59 ? C6 ANP 600 B 1 HETATM 27 N N6 ANP . . . V 7 -1.012 18.34 25.827 1 225.34 ? N6 ANP 600 B 1 HETATM 28 N N1 ANP . . . V 7 -3.137 17.957 24.756 1 226.83 ? N1 ANP 600 B 1 HETATM 29 C C2 ANP . . . V 7 -3.888 17.488 23.733 1 227.08 ? C2 ANP 600 B 1 HETATM 30 N N3 ANP . . . V 7 -3.302 16.88 22.651 1 226.02 ? N3 ANP 600 B 1 HETATM 31 C C4 ANP . . . V 7 -1.957 16.731 22.578 1 223.53 ? C4 ANP 600 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 75 _model_server_stats.query_time_ms 692 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #