data_5LD2 # _model_server_result.job_id TZXWKDGRVJyPTWGdY3cPwA _model_server_result.datetime_utc '2024-12-26 15:04:57' _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 5ld2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1501}' # _entry.id 5LD2 # _exptl.entry_id 5LD2 _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 5LD2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LD2 _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 _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 metalc ? metalc1 A OG1 THR 31 B THR 30 1_555 F MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc2 A OE2 GLU 386 B GLU 385 1_555 F MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc3 E O2G ANP . B ANP 1501 1_555 F MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc4 E O2B ANP . B ANP 1501 1_555 F MG MG . B MG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? hydrog WATSON-CRICK hydrog1 D N3 DT 13 X DT 13 1_555 D N1 DA 67 X DA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D O4 DT 13 X DT 13 1_555 D N6 DA 67 X DA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N3 DC 14 X DC 14 1_555 D N1 DG 66 X DG 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N4 DC 14 X DC 14 1_555 D O6 DG 66 X DG 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D O2 DC 14 X DC 14 1_555 D N2 DG 66 X DG 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N3 DT 15 X DT 15 1_555 D N1 DA 65 X DA 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D O4 DT 15 X DT 15 1_555 D N6 DA 65 X DA 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N1 DA 16 X DA 16 1_555 D N3 DT 64 X DT 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N6 DA 16 X DA 16 1_555 D O4 DT 64 X DT 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N1 DA 17 X DA 17 1_555 D N3 DT 63 X DT 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N6 DA 17 X DA 17 1_555 D O4 DT 63 X DT 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N3 DT 18 X DT 18 1_555 D N1 DA 62 X DA 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D O4 DT 18 X DT 18 1_555 D N6 DA 62 X DA 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N1 DG 19 X DG 19 1_555 D N3 DC 61 X DC 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N2 DG 19 X DG 19 1_555 D O2 DC 61 X DC 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D O6 DG 19 X DG 19 1_555 D N4 DC 61 X DC 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 DC 20 X DC 20 1_555 D N1 DG 60 X DG 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D N4 DC 20 X DC 20 1_555 D O6 DG 60 X DG 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D O2 DC 20 X DC 20 1_555 D N2 DG 60 X DG 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N1 DG 21 X DG 21 1_555 D N3 DC 59 X DC 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D N2 DG 21 X DG 21 1_555 D O2 DC 59 X DC 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D O6 DG 21 X DG 21 1_555 D N4 DC 59 X DC 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N1 DA 22 X DA 22 1_555 D N3 DT 58 X DT 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N6 DA 22 X DA 22 1_555 D O4 DT 58 X DT 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N1 DG 23 X DG 23 1_555 D N3 DC 57 X DC 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N2 DG 23 X DG 23 1_555 D O2 DC 57 X DC 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D O6 DG 23 X DG 23 1_555 D N4 DC 57 X DC 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D N3 DC 24 X DC 24 1_555 D N1 DG 56 X DG 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N4 DC 24 X DC 24 1_555 D O6 DG 56 X DG 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D O2 DC 24 X DC 24 1_555 D N2 DG 56 X DG 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D N1 DA 25 X DA 25 1_555 D N3 DT 55 X DT 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D N6 DA 25 X DA 25 1_555 D O4 DT 55 X DT 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D N3 DC 26 X DC 26 1_555 D N1 DG 54 X DG 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D N4 DC 26 X DC 26 1_555 D O6 DG 54 X DG 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 D O2 DC 26 X DC 26 1_555 D N2 DG 54 X DG 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 D N3 DT 27 X DT 27 1_555 D N1 DA 53 X DA 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 D O4 DT 27 X DT 27 1_555 D N6 DA 53 X DA 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 D N1 DG 28 X DG 28 1_555 D N3 DC 52 X DC 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D N2 DG 28 X DG 28 1_555 D O2 DC 52 X DC 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D O6 DG 28 X DG 28 1_555 D N4 DC 52 X DC 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D N3 DC 29 X DC 29 1_555 D N1 DG 51 X DG 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D N4 DC 29 X DC 29 1_555 D O6 DG 51 X DG 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D O2 DC 29 X DC 29 1_555 D N2 DG 51 X DG 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 D N3 DT 30 X DT 30 1_555 D N1 DA 50 X DA 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 D O4 DT 30 X DT 30 1_555 D N6 DA 50 X DA 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5LD2 _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 B 1 1501 1501 ANP ANP . F 6 MG B 1 1502 1503 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 5 156.117 109.197 103.283 1 93.63 ? PG ANP 1501 B 1 HETATM 2 O O1G ANP . . . E 5 156.094 110.692 103.112 1 99.97 ? O1G ANP 1501 B 1 HETATM 3 O O2G ANP . . . E 5 154.764 108.627 103.663 1 102.04 ? O2G ANP 1501 B 1 HETATM 4 O O3G ANP . . . E 5 157.311 108.737 104.081 1 91.44 ? O3G ANP 1501 B 1 HETATM 5 P PB ANP . . . E 5 156.655 106.747 101.827 1 88.86 ? PB ANP 1501 B 1 HETATM 6 O O1B ANP . . . E 5 157.794 106.279 102.445 1 87.86 ? O1B ANP 1501 B 1 HETATM 7 O O2B ANP . . . E 5 155.33 106.23 102.489 1 89.6 ? O2B ANP 1501 B 1 HETATM 8 N N3B ANP . . . E 5 156.611 108.483 101.744 1 86.53 ? N3B ANP 1501 B 1 HETATM 9 P PA ANP . . . E 5 155.547 106.218 99.503 1 113.85 ? PA ANP 1501 B 1 HETATM 10 O O1A ANP . . . E 5 155.037 104.811 99.741 1 106.7 ? O1A ANP 1501 B 1 HETATM 11 O O2A ANP . . . E 5 154.689 107.412 99.885 1 110.58 ? O2A ANP 1501 B 1 HETATM 12 O O3A ANP . . . E 5 156.785 106.346 100.339 1 99.22 ? O3A ANP 1501 B 1 HETATM 13 O O5' ANP . . . E 5 156.003 106.324 97.954 1 106.62 ? O5' ANP 1501 B 1 HETATM 14 C C5' ANP . . . E 5 156.532 107.534 97.388 1 99.31 ? C5' ANP 1501 B 1 HETATM 15 C C4' ANP . . . E 5 156.325 107.63 95.871 1 92.02 ? C4' ANP 1501 B 1 HETATM 16 O O4' ANP . . . E 5 157.18 106.751 95.127 1 93.91 ? O4' ANP 1501 B 1 HETATM 17 C C3' ANP . . . E 5 154.919 107.272 95.453 1 96.03 ? C3' ANP 1501 B 1 HETATM 18 O O3' ANP . . . E 5 154.508 108.382 94.638 1 90.68 ? O3' ANP 1501 B 1 HETATM 19 C C2' ANP . . . E 5 155.053 105.864 94.821 1 91.54 ? C2' ANP 1501 B 1 HETATM 20 O O2' ANP . . . E 5 154.243 105.53 93.695 1 102.43 ? O2' ANP 1501 B 1 HETATM 21 C C1' ANP . . . E 5 156.473 105.779 94.34 1 86.62 ? C1' ANP 1501 B 1 HETATM 22 N N9 ANP . . . E 5 157.069 104.444 94.563 1 82.17 ? N9 ANP 1501 B 1 HETATM 23 C C8 ANP . . . E 5 157.437 103.982 95.763 1 91.17 ? C8 ANP 1501 B 1 HETATM 24 N N7 ANP . . . E 5 157.993 102.748 95.693 1 94.41 ? N7 ANP 1501 B 1 HETATM 25 C C5 ANP . . . E 5 158.007 102.39 94.41 1 88.84 ? C5 ANP 1501 B 1 HETATM 26 C C6 ANP . . . E 5 158.474 101.189 93.666 1 88.48 ? C6 ANP 1501 B 1 HETATM 27 N N6 ANP . . . E 5 159.034 100.136 94.311 1 83.24 ? N6 ANP 1501 B 1 HETATM 28 N N1 ANP . . . E 5 158.305 101.192 92.323 1 95.43 ? N1 ANP 1501 B 1 HETATM 29 C C2 ANP . . . E 5 157.738 102.259 91.696 1 107.55 ? C2 ANP 1501 B 1 HETATM 30 N N3 ANP . . . E 5 157.305 103.392 92.319 1 99.95 ? N3 ANP 1501 B 1 HETATM 31 C C4 ANP . . . E 5 157.405 103.52 93.663 1 87.87 ? C4 ANP 1501 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 434 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #