data_5A3Q # _model_server_result.job_id tY5AvfRbbH7HDgWG-YcoBA _model_server_result.datetime_utc '2024-11-06 07:42:19' _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 5a3q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 5A3Q # _exptl.entry_id 5A3Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 716.297 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate" _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 5A3Q _cell.length_a 86.427 _cell.length_b 118.781 _cell.length_c 141.828 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A3Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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,G,H,I _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 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A OE1 GLN 245 A GLN 244 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc2 A OD1 ASP 352 A ASP 351 1_555 C V VN4 . A VN4 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc3 A OD2 ASP 352 A ASP 351 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 A O THR 354 A THR 353 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc5 A OD1 ASN 629 A ASN 628 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 A OD1 ASP 704 A ASP 703 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc7 A O LEU 712 A LEU 711 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc8 A O LYS 713 A LYS 712 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc9 A O ALA 715 A ALA 714 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc10 A OE1 GLU 733 A GLU 732 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc11 A OE2 GLU 733 A GLU 732 1_555 G K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc12 C O2 VN4 . A VN4 1001 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc13 C V VN4 . A VN4 1001 1_555 I O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc14 D O2B DL5 . A DL5 1002 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc15 D O1G DL5 . A DL5 1002 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? metalc ? metalc16 E MG MG . A MG 1003 1_555 I O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc17 E MG MG . A MG 1003 1_555 I O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc18 F MG MG . A MG 1004 1_555 I O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? metalc ? metalc19 G K K . A K 1008 1_555 I O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.4 ? # _chem_comp.formula 'C17 H19 N8 O18 P3' _chem_comp.formula_weight 716.297 _chem_comp.id DL5 _chem_comp.mon_nstd_flag . _chem_comp.name "Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TNP-AMPPCP # 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 C2 N1 DL5 doub 89 n y C6 N1 DL5 sing 90 n y N3 C2 DL5 sing 91 n y C2 H2 DL5 sing 92 n n C4 N3 DL5 doub 93 n y N9 C4 DL5 sing 94 n y C4 C5 DL5 sing 95 n y N7 C5 DL5 sing 96 n y C5 C6 DL5 doub 97 n y C6 N6 DL5 sing 98 n n N6 HN6 DL5 sing 99 n n N6 HN6A DL5 sing 100 n n C8 N7 DL5 doub 101 n y N9 C8 DL5 sing 102 n y C8 H8 DL5 sing 103 n n C1' N9 DL5 sing 104 n n O1A PA DL5 doub 105 n n O2A PA DL5 sing 106 n n PA O3A DL5 sing 107 n n PA O5' DL5 sing 108 n n O3A PB DL5 sing 109 n n O2B PB DL5 doub 110 n n PB O1B DL5 sing 111 n n PB C01 DL5 sing 112 n n O1G PG DL5 doub 113 n n O3G PG DL5 sing 114 n n PG C01 DL5 sing 115 n n PG O2G DL5 sing 116 n n C01 H01 DL5 sing 117 n n C01 H01A DL5 sing 118 n n C2' C1' DL5 sing 119 n n C1' O4' DL5 sing 120 n n C1' H1' DL5 sing 121 n n O1B HO1B DL5 sing 122 n n C2F C1F DL5 sing 123 n n O3' C1F DL5 sing 124 n n C1F O2' DL5 sing 125 n n C1F C6F DL5 sing 126 n n C3' C2' DL5 sing 127 n n O2' C2' DL5 sing 128 n n C2' H2' DL5 sing 129 n n O2A HO2A DL5 sing 130 n n N2F C2F DL5 sing 131 n n C3F C2F DL5 doub 132 n n O2F N2F DL5 doub 133 n n O3F N2F DL5 sing 134 n n O2G HO2G DL5 sing 135 n n O3' C3' DL5 sing 136 n n C3' C4' DL5 sing 137 n n C3' H3' DL5 sing 138 n n C3F C4F DL5 sing 139 n n C3F H3F DL5 sing 140 n n O3G HO3G DL5 sing 141 n n C5' C4' DL5 sing 142 n n C4' O4' DL5 sing 143 n n C4' H4' DL5 sing 144 n n N4F C4F DL5 doub 145 n n C4F C5F DL5 sing 146 n n O5F N4F DL5 sing 147 n n N4F O4F DL5 sing 148 n n O5' C5' DL5 sing 149 n n C5' H5' DL5 sing 150 n n C5' "H5'A" DL5 sing 151 n n C5F C6F DL5 doub 152 n n C5F H5F DL5 sing 153 n n C6F N6F DL5 sing 154 n n N6F O7F DL5 sing 155 n n N6F O6F DL5 doub 156 n n H4F O4F DL5 sing 157 n n # _atom_sites.entry_id 5A3Q _atom_sites.fract_transf_matrix[1][1] 0.01157 _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] 0.008419 _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] 0.007051 _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 B 2 TG1 A 1 1000 1000 TG1 TG1 . C 3 VN4 A 1 1001 1001 VN4 VN4 . D 4 DL5 A 1 1002 1002 DL5 DL5 . E 5 MG A 1 1003 1003 MG MG . F 5 MG A 1 1004 1004 MG MG . G 6 K A 1 1008 1008 K K . H 7 CL A 1 1009 1009 CL CL . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . # 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 N N1 DL5 . . . D 4 20.39 16.698 -7.802 1 98.36 ? N1 DL5 1002 A 1 HETATM 2 C C2 DL5 . . . D 4 21.461 16.436 -7.052 1 100.03 ? C2 DL5 1002 A 1 HETATM 3 N N3 DL5 . . . D 4 22.007 15.265 -6.726 1 95.92 ? N3 DL5 1002 A 1 HETATM 4 C C4 DL5 . . . D 4 21.326 14.246 -7.268 1 93.01 ? C4 DL5 1002 A 1 HETATM 5 C C5 DL5 . . . D 4 20.193 14.337 -8.071 1 96.4 ? C5 DL5 1002 A 1 HETATM 6 C C6 DL5 . . . D 4 19.713 15.664 -8.34 1 99.62 ? C6 DL5 1002 A 1 HETATM 7 N N6 DL5 . . . D 4 18.627 15.903 -9.102 1 121.63 ? N6 DL5 1002 A 1 HETATM 8 N N7 DL5 . . . D 4 19.759 13.072 -8.446 1 95.26 ? N7 DL5 1002 A 1 HETATM 9 C C8 DL5 . . . D 4 20.622 12.288 -7.878 1 94.78 ? C8 DL5 1002 A 1 HETATM 10 N N9 DL5 . . . D 4 21.591 12.913 -7.152 1 95.57 ? N9 DL5 1002 A 1 HETATM 11 P PA DL5 . . . D 4 19.895 7.731 -7.612 1 101.58 ? PA DL5 1002 A 1 HETATM 12 P PB DL5 . . . D 4 17.684 9.389 -6.521 1 119.73 ? PB DL5 1002 A 1 HETATM 13 P PG DL5 . . . D 4 15.146 8.624 -8.068 1 132.65 ? PG DL5 1002 A 1 HETATM 14 C C01 DL5 . . . D 4 16.162 8.418 -6.612 1 131.67 ? C01 DL5 1002 A 1 HETATM 15 C C1' DL5 . . . D 4 22.719 12.294 -6.381 1 95.34 ? C1' DL5 1002 A 1 HETATM 16 O O1A DL5 . . . D 4 19.644 6.167 -7.536 1 108.89 ? O1A DL5 1002 A 1 HETATM 17 O O1B DL5 . . . D 4 17.734 10.161 -5.171 1 123.81 ? O1B DL5 1002 A 1 HETATM 18 C C1F DL5 . . . D 4 23.839 10.887 -3.427 1 116.15 ? C1F DL5 1002 A 1 HETATM 19 O O1G DL5 . . . D 4 15.513 9.96 -8.734 1 160.26 ? O1G DL5 1002 A 1 HETATM 20 C C2' DL5 . . . D 4 22.296 11.617 -5.056 1 100.19 ? C2' DL5 1002 A 1 HETATM 21 O O2' DL5 . . . D 4 23.17 12.022 -3.961 1 114.78 ? O2' DL5 1002 A 1 HETATM 22 O O2A DL5 . . . D 4 19.617 8.432 -8.923 1 101.87 ? O2A DL5 1002 A 1 HETATM 23 O O2B DL5 . . . D 4 17.688 10.375 -7.67 1 117 ? O2B DL5 1002 A 1 HETATM 24 C C2F DL5 . . . D 4 23.339 10.719 -1.985 1 126.54 ? C2F DL5 1002 A 1 HETATM 25 N N2F DL5 . . . D 4 21.919 10.623 -1.663 1 137.06 ? N2F DL5 1002 A 1 HETATM 26 O O2F DL5 . . . D 4 21.622 10.479 -0.514 1 139.77 ? O2F DL5 1002 A 1 HETATM 27 O O2G DL5 . . . D 4 15.612 7.48 -9.064 1 145.62 ? O2G DL5 1002 A 1 HETATM 28 C C3' DL5 . . . D 4 22.483 10.112 -5.209 1 97.48 ? C3' DL5 1002 A 1 HETATM 29 O O3' DL5 . . . D 4 23.459 9.737 -4.193 1 103.85 ? O3' DL5 1002 A 1 HETATM 30 O O3A DL5 . . . D 4 18.918 8.411 -6.499 1 114.69 ? O3A DL5 1002 A 1 HETATM 31 C C3F DL5 . . . D 4 24.176 10.629 -0.915 1 122.1 ? C3F DL5 1002 A 1 HETATM 32 O O3F DL5 . . . D 4 21.078 10.689 -2.548 1 141.32 ? O3F DL5 1002 A 1 HETATM 33 O O3G DL5 . . . D 4 13.689 8.467 -7.763 1 144.64 ? O3G DL5 1002 A 1 HETATM 34 C C4' DL5 . . . D 4 23.033 9.922 -6.617 1 96.33 ? C4' DL5 1002 A 1 HETATM 35 O O4' DL5 . . . D 4 23.145 11.267 -7.213 1 96.79 ? O4' DL5 1002 A 1 HETATM 36 C C4F DL5 . . . D 4 25.561 10.688 -0.959 1 121.29 ? C4F DL5 1002 A 1 HETATM 37 N N4F DL5 . . . D 4 26.362 10.577 0.238 1 122.85 ? N4F DL5 1002 A 1 HETATM 38 O O4F DL5 . . . D 4 27.581 10.636 0.127 1 119.78 ? O4F DL5 1002 A 1 HETATM 39 C C5' DL5 . . . D 4 22.185 9.162 -7.607 1 94.47 ? C5' DL5 1002 A 1 HETATM 40 O O5' DL5 . . . D 4 21.384 8.129 -6.986 1 99.05 ? O5' DL5 1002 A 1 HETATM 41 C C5F DL5 . . . D 4 26.148 10.845 -2.132 1 115.14 ? C5F DL5 1002 A 1 HETATM 42 O O5F DL5 . . . D 4 25.804 10.431 1.306 1 127.28 ? O5F DL5 1002 A 1 HETATM 43 C C6F DL5 . . . D 4 25.391 10.97 -3.433 1 111.81 ? C6F DL5 1002 A 1 HETATM 44 N N6F DL5 . . . D 4 26.16 11.145 -4.742 1 117.41 ? N6F DL5 1002 A 1 HETATM 45 O O6F DL5 . . . D 4 27.407 11.193 -4.722 1 116.73 ? O6F DL5 1002 A 1 HETATM 46 O O7F DL5 . . . D 4 25.525 11.239 -5.77 1 133.41 ? O7F DL5 1002 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 379 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #