data_1S76 # _model_server_result.job_id vWr2Uck2pj1QSBhCXU4PHw _model_server_result.datetime_utc '2025-02-27 06:23:06' _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 1s76 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 1S76 # _exptl.entry_id 1S76 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL 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 1S76 _cell.length_a 138.72 _cell.length_b 143.32 _cell.length_c 146.65 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S76 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 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 E O2B APC . R APC 901 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc2 E O2A APC . R APC 901 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? metalc ? metalc3 E O2A APC . R APC 901 1_555 G MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc4 D OD2 ASP 537 D ASP 537 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc5 D OD1 ASP 537 D ASP 537 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc6 D OD1 ASP 537 D ASP 537 1_555 G MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc7 D O GLY 538 D GLY 538 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? metalc ? metalc8 D OD1 ASP 812 D ASP 812 1_555 F MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc9 D OD2 ASP 812 D ASP 812 1_555 G MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc10 F MG MG . D MG 902 1_555 G MG MG . D MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? hydrog 'DG-DC PAIR' hydrog1 A N1 DG 1 T DG 130 1_555 B N3 DC 17 N DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DA MISPAIR' hydrog2 A N2 DG 4 T DG 127 1_555 B N1 DA 13 N DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog3 A N4 DC 7 T DC 124 1_555 B O6 DG 11 N DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 12 T DT 119 1_555 C N1 A 9 R A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 12 T DT 119 1_555 C N6 A 9 R A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DC 13 T DC 118 1_555 C N1 G 8 R G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 DC 13 T DC 118 1_555 C O6 G 8 R G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 DC 13 T DC 118 1_555 C N2 G 8 R G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DG 14 T DG 117 1_555 C N3 C 7 R C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 DG 14 T DG 117 1_555 C O2 C 7 R C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 DG 14 T DG 117 1_555 C N4 C 7 R C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 15 T DC 116 1_555 C N1 G 6 R G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 15 T DC 116 1_555 C O6 G 6 R G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 15 T DC 116 1_555 C N2 G 6 R G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 16 T DC 115 1_555 C N1 G 5 R G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 16 T DC 115 1_555 C O6 G 5 R G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 16 T DC 115 1_555 C N2 G 5 R G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 DG 17 T DG 114 1_555 C N3 C 4 R C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 DG 17 T DG 114 1_555 C O2 C 4 R C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 DG 17 T DG 114 1_555 C N4 C 4 R C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 APC doub 52 n n PG O2G APC sing 53 n n PG O3G APC sing 54 n n PG O3B APC sing 55 n n O2G HOG2 APC sing 56 n n O3G HOG3 APC sing 57 n n PB O1B APC doub 58 n n PB O2B APC sing 59 n n PB O3B APC sing 60 n n PB C3A APC sing 61 n n O2B HOB2 APC sing 62 n n PA O1A APC doub 63 n n PA O2A APC sing 64 n n PA C3A APC sing 65 n n PA O5' APC sing 66 n n O2A HOA2 APC sing 67 n n C3A H3A1 APC sing 68 n n C3A H3A2 APC sing 69 n n O5' C5' APC sing 70 n n C5' C4' APC sing 71 n n C5' "H5'1" APC sing 72 n n C5' "H5'2" APC sing 73 n n C4' O4' APC sing 74 n n C4' C3' APC sing 75 n n C4' H4' APC sing 76 n n O4' C1' APC sing 77 n n C3' O3' APC sing 78 n n C3' C2' APC sing 79 n n C3' H3' APC sing 80 n n O3' HO3' APC sing 81 n n C2' O2' APC sing 82 n n C2' C1' APC sing 83 n n C2' H2' APC sing 84 n n O2' HO2' APC sing 85 n n C1' N9 APC sing 86 n n C1' H1' APC sing 87 n n N9 C8 APC sing 88 n y N9 C4 APC sing 89 n y C8 N7 APC doub 90 n y C8 H8 APC sing 91 n n N7 C5 APC sing 92 n y C5 C6 APC sing 93 n y C5 C4 APC doub 94 n y C6 N6 APC sing 95 n n C6 N1 APC doub 96 n y N6 HN61 APC sing 97 n n N6 HN62 APC sing 98 n n N1 C2 APC sing 99 n y C2 N3 APC doub 100 n y C2 H2 APC sing 101 n n N3 C4 APC sing 102 n y # _atom_sites.entry_id 1S76 _atom_sites.fract_transf_matrix[1][1] 0.007209 _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] 0.006977 _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] 0.006819 _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 APC R 1 901 901 APC APC . F 6 MG D 1 902 902 MG MG . G 6 MG D 1 903 903 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 APC . . . E 5 -43.41 5.262 42.813 1 23.58 ? PG APC 901 R 1 HETATM 2 O O1G APC . . . E 5 -42.18 4.871 43.541 1 27.58 ? O1G APC 901 R 1 HETATM 3 O O2G APC . . . E 5 -44.72 4.689 43.224 1 23.7 ? O2G APC 901 R 1 HETATM 4 O O3G APC . . . E 5 -43.198 5.001 41.246 1 22.16 ? O3G APC 901 R 1 HETATM 5 P PB APC . . . E 5 -43.122 8.029 43.86 1 20.03 ? PB APC 901 R 1 HETATM 6 O O1B APC . . . E 5 -44.191 9.033 43.702 1 26.25 ? O1B APC 901 R 1 HETATM 7 O O2B APC . . . E 5 -42.888 7.423 45.194 1 20.73 ? O2B APC 901 R 1 HETATM 8 O O3B APC . . . E 5 -43.481 6.879 42.772 1 33.18 ? O3B APC 901 R 1 HETATM 9 P PA APC . . . E 5 -40.223 9.04 43.245 1 21.87 ? PA APC 901 R 1 HETATM 10 O O1A APC . . . E 5 -39.724 8.719 41.889 1 13.56 ? O1A APC 901 R 1 HETATM 11 O O2A APC . . . E 5 -39.943 8.116 44.371 1 22.83 ? O2A APC 901 R 1 HETATM 12 C C3A APC . . . E 5 -41.904 8.991 43.269 1 23.57 ? C3A APC 901 R 1 HETATM 13 O O5' APC . . . E 5 -39.67 10.482 43.608 1 15.38 ? O5' APC 901 R 1 HETATM 14 C C5' APC . . . E 5 -39.735 10.999 44.948 1 19.16 ? C5' APC 901 R 1 HETATM 15 C C4' APC . . . E 5 -40.4 12.358 44.939 1 17.03 ? C4' APC 901 R 1 HETATM 16 O O4' APC . . . E 5 -39.606 13.284 44.145 1 15.78 ? O4' APC 901 R 1 HETATM 17 C C3' APC . . . E 5 -41.776 12.392 44.293 1 14.49 ? C3' APC 901 R 1 HETATM 18 O O3' APC . . . E 5 -42.823 11.889 45.034 1 67.51 ? O3' APC 901 R 1 HETATM 19 C C2' APC . . . E 5 -41.902 13.85 43.88 1 14.47 ? C2' APC 901 R 1 HETATM 20 O O2' APC . . . E 5 -42.483 14.74 44.896 1 67.51 ? O2' APC 901 R 1 HETATM 21 C C1' APC . . . E 5 -40.465 14.19 43.478 1 17.43 ? C1' APC 901 R 1 HETATM 22 N N9 APC . . . E 5 -40.141 14.182 42.089 1 44.05 ? N9 APC 901 R 1 HETATM 23 C C8 APC . . . E 5 -39.591 12.995 41.669 1 41.02 ? C8 APC 901 R 1 HETATM 24 N N7 APC . . . E 5 -39.461 12.91 40.363 1 37.84 ? N7 APC 901 R 1 HETATM 25 C C5 APC . . . E 5 -39.944 14.131 39.9 1 35.3 ? C5 APC 901 R 1 HETATM 26 C C6 APC . . . E 5 -40.095 14.665 38.608 1 32.6 ? C6 APC 901 R 1 HETATM 27 N N6 APC . . . E 5 -39.771 14.008 37.496 1 30.5 ? N6 APC 901 R 1 HETATM 28 N N1 APC . . . E 5 -40.603 15.912 38.497 1 30.42 ? N1 APC 901 R 1 HETATM 29 C C2 APC . . . E 5 -40.939 16.57 39.608 1 32.04 ? C2 APC 901 R 1 HETATM 30 N N3 APC . . . E 5 -40.853 16.172 40.877 1 36.09 ? N3 APC 901 R 1 HETATM 31 C C4 APC . . . E 5 -40.343 14.929 40.953 1 37.75 ? C4 APC 901 R 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #