data_4RIY # _model_server_result.job_id MH5bcAV-TvJBFIf8vu5Bgg _model_server_result.datetime_utc '2025-07-31 14:37:59' _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 4riy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1101}' # _entry.id 4RIY # _exptl.entry_id 4RIY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _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 110.93 _cell.angle_gamma 90 _cell.entry_id 4RIY _cell.length_a 65.334 _cell.length_b 155.14 _cell.length_c 87.297 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RIY _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H 1 1 C,D,I,J,K,L 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 ? 3 E N N ? 3 I 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 OD1 ASN 145 A ASN 820 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc2 A OD2 ASP 158 A ASP 833 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc3 E O3A ANP . A ANP 1101 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 E O2A ANP . A ANP 1101 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc5 E O3G ANP . A ANP 1101 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc6 B OD1 ASN 165 B ASN 818 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc7 G O2B ADP . B ADP 1001 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc8 C OD1 ASN 145 C ASN 820 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc9 C OD2 ASP 158 C ASP 833 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc10 I O2A ANP . C ANP 1101 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc11 I O3A ANP . C ANP 1101 1_555 J MG MG . C MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc12 D OD1 ASN 165 D ASN 818 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc13 K O2B ADP . D ADP 1001 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc14 K O2A ADP . D ADP 1001 1_555 L MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? # _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 57 n n PG O2G ANP sing 58 n n PG O3G ANP sing 59 n n PG N3B ANP sing 60 n n O2G HOG2 ANP sing 61 n n O3G HOG3 ANP sing 62 n n PB O1B ANP doub 63 n n PB O2B ANP sing 64 n n PB N3B ANP sing 65 n n PB O3A ANP sing 66 n n O2B HOB2 ANP sing 67 n n N3B HNB1 ANP sing 68 n n PA O1A ANP doub 69 n n PA O2A ANP sing 70 n n PA O3A ANP sing 71 n n PA O5' ANP sing 72 n n O2A HOA2 ANP sing 73 n n O5' C5' ANP sing 74 n n C5' C4' ANP sing 75 n n C5' "H5'1" ANP sing 76 n n C5' "H5'2" ANP sing 77 n n C4' O4' ANP sing 78 n n C4' C3' ANP sing 79 n n C4' H4' ANP sing 80 n n O4' C1' ANP sing 81 n n C3' O3' ANP sing 82 n n C3' C2' ANP sing 83 n n C3' H3' ANP sing 84 n n O3' HO3' ANP sing 85 n n C2' O2' ANP sing 86 n n C2' C1' ANP sing 87 n n C2' H2' ANP sing 88 n n O2' HO2' ANP sing 89 n n C1' N9 ANP sing 90 n n C1' H1' ANP sing 91 n n N9 C8 ANP sing 92 n y N9 C4 ANP sing 93 n y C8 N7 ANP doub 94 n y C8 H8 ANP sing 95 n n N7 C5 ANP sing 96 n y C5 C6 ANP sing 97 n y C5 C4 ANP doub 98 n y C6 N6 ANP sing 99 n n C6 N1 ANP doub 100 n y N6 HN61 ANP sing 101 n n N6 HN62 ANP sing 102 n n N1 C2 ANP sing 103 n y C2 N3 ANP doub 104 n y C2 H2 ANP sing 105 n n N3 C4 ANP sing 106 n y # _atom_sites.entry_id 4RIY _atom_sites.fract_transf_matrix[1][1] 0.015306 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005854 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006446 _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] 0.012264 _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 3 ANP A 1 1101 1 ANP ANP . F 4 MG A 1 1102 2 MG MG . G 5 ADP B 1 1001 1 ADP ADP . H 4 MG B 1 1002 2 MG MG . I 3 ANP C 1 1101 1 ANP ANP . J 4 MG C 1 1102 2 MG MG . K 5 ADP D 1 1001 1 ADP ADP . L 4 MG D 1 1002 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 . . . I 3 44.713 20.539 -47.979 1 25 ? PG ANP 1101 C 1 HETATM 2 O O1G ANP . . . I 3 46.183 20.804 -47.892 1 30.18 ? O1G ANP 1101 C 1 HETATM 3 O O2G ANP . . . I 3 44.48 18.979 -47.917 1 26.39 ? O2G ANP 1101 C 1 HETATM 4 O O3G ANP . . . I 3 44.165 21.092 -49.356 1 26.88 ? O3G ANP 1101 C 1 HETATM 5 P PB ANP . . . I 3 44.821 22.365 -45.812 1 17.32 ? PB ANP 1101 C 1 HETATM 6 O O1B ANP . . . I 3 44.576 22.157 -44.352 1 19.17 ? O1B ANP 1101 C 1 HETATM 7 O O2B ANP . . . I 3 46.333 22.133 -46.09 1 79.71 ? O2B ANP 1101 C 1 HETATM 8 N N3B ANP . . . I 3 43.88 21.286 -46.7 1 38.15 ? N3B ANP 1101 C 1 HETATM 9 P PA ANP . . . I 3 45.141 24.694 -47.283 1 34.2 ? PA ANP 1101 C 1 HETATM 10 O O1A ANP . . . I 3 46.525 24.225 -47.538 1 34.15 -1 O1A ANP 1101 C 1 HETATM 11 O O2A ANP . . . I 3 44.242 24.686 -48.522 1 31.36 ? O2A ANP 1101 C 1 HETATM 12 O O3A ANP . . . I 3 44.41 23.831 -46.166 1 67.25 ? O3A ANP 1101 C 1 HETATM 13 O O5' ANP . . . I 3 45.22 26.138 -46.626 1 47.13 ? O5' ANP 1101 C 1 HETATM 14 C C5' ANP . . . I 3 45.927 26.363 -45.389 1 42 ? C5' ANP 1101 C 1 HETATM 15 C C4' ANP . . . I 3 45.032 27.069 -44.398 1 37 ? C4' ANP 1101 C 1 HETATM 16 O O4' ANP . . . I 3 44.053 27.879 -45.09 1 36.41 ? O4' ANP 1101 C 1 HETATM 17 C C3' ANP . . . I 3 44.256 26.16 -43.441 1 25.81 ? C3' ANP 1101 C 1 HETATM 18 O O3' ANP . . . I 3 44.494 26.542 -42.09 1 19.03 ? O3' ANP 1101 C 1 HETATM 19 C C2' ANP . . . I 3 42.791 26.381 -43.839 1 26.24 ? C2' ANP 1101 C 1 HETATM 20 O O2' ANP . . . I 3 41.904 26.272 -42.732 1 26.02 ? O2' ANP 1101 C 1 HETATM 21 C C1' ANP . . . I 3 42.846 27.809 -44.365 1 31.04 ? C1' ANP 1101 C 1 HETATM 22 N N9 ANP . . . I 3 41.731 28.165 -45.246 1 31.4 ? N9 ANP 1101 C 1 HETATM 23 C C8 ANP . . . I 3 41.454 27.633 -46.482 1 32.33 ? C8 ANP 1101 C 1 HETATM 24 N N7 ANP . . . I 3 40.382 28.146 -47.019 1 33.36 ? N7 ANP 1101 C 1 HETATM 25 C C5 ANP . . . I 3 39.904 29.061 -46.111 1 33.36 ? C5 ANP 1101 C 1 HETATM 26 C C6 ANP . . . I 3 38.812 29.928 -46.082 1 36.48 ? C6 ANP 1101 C 1 HETATM 27 N N6 ANP . . . I 3 37.925 30.018 -47.084 1 43.75 ? N6 ANP 1101 C 1 HETATM 28 N N1 ANP . . . I 3 38.638 30.713 -44.997 1 29.03 ? N1 ANP 1101 C 1 HETATM 29 C C2 ANP . . . I 3 39.522 30.625 -43.998 1 28.2 ? C2 ANP 1101 C 1 HETATM 30 N N3 ANP . . . I 3 40.601 29.844 -43.901 1 28.13 ? N3 ANP 1101 C 1 HETATM 31 C C4 ANP . . . I 3 40.75 29.079 -44.982 1 31.21 ? C4 ANP 1101 C 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 92 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #