data_4JRN # _model_server_result.job_id ei0-cyCRZY4qkU4uoVRnXA _model_server_result.datetime_utc '2025-03-06 01:37:09' _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 4jrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 4JRN # _exptl.entry_id 4JRN _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 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 120 _cell.entry_id 4JRN _cell.length_a 48.65 _cell.length_b 48.65 _cell.length_c 293.746 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JRN _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC D 1 SUC 2 n B FRU 2 B 2 FRU D 1 SUC # 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 disulf ? disulf1 A SG CYS 296 A CYS 478 1_555 A SG CYS 315 A CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 B C1 GLC . B GLC 1 1_555 B O2 FRU . B FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 sing metalc ? metalc1 A OD2 ASP 245 A ASP 427 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc2 A OD1 ASP 245 A ASP 427 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc3 C O3G ANP . A ANP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc4 C O1G ANP . A ANP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc5 C O2B ANP . A ANP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? # _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 4JRN _atom_sites.fract_transf_matrix[1][1] 0.020555 _atom_sites.fract_transf_matrix[1][2] 0.011867 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023735 _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] 0.003404 _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 C 3 ANP A 1 601 1 ANP ANP . D 4 MG A 1 602 2 MG MG . E 4 MG A 1 603 3 MG MG . F 5 HOH A 1 701 1 HOH WAT . F 5 HOH A 2 702 2 HOH WAT . F 5 HOH A 3 703 3 HOH WAT . F 5 HOH A 4 704 4 HOH WAT . F 5 HOH A 5 705 5 HOH WAT . F 5 HOH A 6 706 6 HOH WAT . F 5 HOH A 7 707 7 HOH WAT . F 5 HOH A 8 708 8 HOH WAT . # 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 . . . C 3 9.016 40.659 19.379 1 68.35 ? PG ANP 601 A 1 HETATM 2 O O1G ANP . . . C 3 8.495 39.327 19.015 1 51.42 ? O1G ANP 601 A 1 HETATM 3 O O2G ANP . . . C 3 10.505 40.412 19.968 1 75.96 ? O2G ANP 601 A 1 HETATM 4 O O3G ANP . . . C 3 8.053 41.294 20.487 1 57.44 ? O3G ANP 601 A 1 HETATM 5 P PB ANP . . . C 3 7.809 42.115 17.047 1 51.02 ? PB ANP 601 A 1 HETATM 6 O O1B ANP . . . C 3 8.121 42.007 15.599 1 72.8 ? O1B ANP 601 A 1 HETATM 7 O O2B ANP . . . C 3 6.535 41.184 17.336 1 68.97 ? O2B ANP 601 A 1 HETATM 8 N N3B ANP . . . C 3 9.196 41.601 17.95 1 72.53 ? N3B ANP 601 A 1 HETATM 9 P PA ANP . . . C 3 7.146 44.375 18.666 1 50.96 ? PA ANP 601 A 1 HETATM 10 O O1A ANP . . . C 3 5.836 43.987 19.269 1 55.55 ? O1A ANP 601 A 1 HETATM 11 O O2A ANP . . . C 3 8.301 44.014 19.681 1 73.26 ? O2A ANP 601 A 1 HETATM 12 O O3A ANP . . . C 3 7.317 43.663 17.221 1 55.64 ? O3A ANP 601 A 1 HETATM 13 O O5' ANP . . . C 3 7.15 45.931 18.35 1 49.15 ? O5' ANP 601 A 1 HETATM 14 C C5' ANP . . . C 3 8.511 46.303 18.527 1 49.05 ? C5' ANP 601 A 1 HETATM 15 C C4' ANP . . . C 3 8.549 47.596 19.344 1 48.18 ? C4' ANP 601 A 1 HETATM 16 O O4' ANP . . . C 3 7.875 48.681 18.645 1 50.06 ? O4' ANP 601 A 1 HETATM 17 C C3' ANP . . . C 3 7.904 47.392 20.758 1 55.74 ? C3' ANP 601 A 1 HETATM 18 O O3' ANP . . . C 3 9.033 47.165 21.593 1 72.65 ? O3' ANP 601 A 1 HETATM 19 C C2' ANP . . . C 3 7.261 48.76 20.982 1 43.64 ? C2' ANP 601 A 1 HETATM 20 O O2' ANP . . . C 3 7.985 49.582 21.887 1 52.19 ? O2' ANP 601 A 1 HETATM 21 C C1' ANP . . . C 3 6.998 49.372 19.578 1 52.56 ? C1' ANP 601 A 1 HETATM 22 N N9 ANP . . . C 3 5.59 49.206 19.135 1 34.2 ? N9 ANP 601 A 1 HETATM 23 C C8 ANP . . . C 3 4.939 48.018 18.888 1 48.79 ? C8 ANP 601 A 1 HETATM 24 N N7 ANP . . . C 3 3.714 48.24 18.519 1 40.84 ? N7 ANP 601 A 1 HETATM 25 C C5 ANP . . . C 3 3.483 49.573 18.499 1 28.49 ? C5 ANP 601 A 1 HETATM 26 C C6 ANP . . . C 3 2.37 50.392 18.188 1 32.46 ? C6 ANP 601 A 1 HETATM 27 N N6 ANP . . . C 3 1.172 49.83 17.798 1 41.99 ? N6 ANP 601 A 1 HETATM 28 N N1 ANP . . . C 3 2.502 51.737 18.281 1 46.2 ? N1 ANP 601 A 1 HETATM 29 C C2 ANP . . . C 3 3.646 52.302 18.656 1 36.26 ? C2 ANP 601 A 1 HETATM 30 N N3 ANP . . . C 3 4.716 51.566 18.957 1 43.05 ? N3 ANP 601 A 1 HETATM 31 C C4 ANP . . . C 3 4.682 50.218 18.894 1 35.68 ? C4 ANP 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #