data_5A3R # _model_server_result.job_id dag2hA2EGuVPXiybg9IaLA _model_server_result.datetime_utc '2024-11-18 21:44:28' _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 5a3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1000}' # _entry.id 5A3R # _exptl.entry_id 5A3R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 716.297 _entity.id 2 _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 5A3R _cell.length_a 57.53 _cell.length_b 114.967 _cell.length_c 227.699 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A3R _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 2 _struct_asym.id B _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 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A C SER 350 A SER 350 1_555 A N BFD 351 A BFD 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C BFD 351 A BFD 351 1_555 A N LYS 352 A LYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OE2 GLU 90 A GLU 90 1_555 E MG MG . A MG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 A OE1 GLN 244 A GLN 244 1_555 C K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc3 A OE1 GLU 309 A GLU 309 1_555 E MG MG . A MG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 A OD2 BFD 351 A BFD 351 1_555 F MG MG . A MG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? metalc ? metalc5 A O THR 353 A THR 353 1_555 F MG MG . A MG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc6 A OD1 ASP 703 A ASP 703 1_555 F MG MG . A MG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc7 A O LEU 711 A LEU 711 1_555 C K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.258 ? metalc ? metalc8 A OE2 GLU 732 A GLU 732 1_555 C K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc9 B O1G DL5 . A DL5 1000 1_555 D MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc10 B O2B DL5 . A DL5 1000 1_555 D MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc11 D MG MG . A MG 1007 1_555 G O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc12 D MG MG . A MG 1007 1_555 G O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc13 F MG MG . A MG 1009 1_555 G O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc14 F MG MG . A MG 1009 1_555 G O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _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 101 n y C6 N1 DL5 sing 102 n y N3 C2 DL5 sing 103 n y C2 H2 DL5 sing 104 n n C4 N3 DL5 doub 105 n y N9 C4 DL5 sing 106 n y C4 C5 DL5 sing 107 n y N7 C5 DL5 sing 108 n y C5 C6 DL5 doub 109 n y C6 N6 DL5 sing 110 n n N6 HN6 DL5 sing 111 n n N6 HN6A DL5 sing 112 n n C8 N7 DL5 doub 113 n y N9 C8 DL5 sing 114 n y C8 H8 DL5 sing 115 n n C1' N9 DL5 sing 116 n n O1A PA DL5 doub 117 n n O2A PA DL5 sing 118 n n PA O3A DL5 sing 119 n n PA O5' DL5 sing 120 n n O3A PB DL5 sing 121 n n O2B PB DL5 doub 122 n n PB O1B DL5 sing 123 n n PB C01 DL5 sing 124 n n O1G PG DL5 doub 125 n n O3G PG DL5 sing 126 n n PG C01 DL5 sing 127 n n PG O2G DL5 sing 128 n n C01 H01 DL5 sing 129 n n C01 H01A DL5 sing 130 n n C2' C1' DL5 sing 131 n n C1' O4' DL5 sing 132 n n C1' H1' DL5 sing 133 n n O1B HO1B DL5 sing 134 n n C2F C1F DL5 sing 135 n n O3' C1F DL5 sing 136 n n C1F O2' DL5 sing 137 n n C1F C6F DL5 sing 138 n n C3' C2' DL5 sing 139 n n O2' C2' DL5 sing 140 n n C2' H2' DL5 sing 141 n n O2A HO2A DL5 sing 142 n n N2F C2F DL5 sing 143 n n C3F C2F DL5 doub 144 n n O2F N2F DL5 doub 145 n n O3F N2F DL5 sing 146 n n O2G HO2G DL5 sing 147 n n O3' C3' DL5 sing 148 n n C3' C4' DL5 sing 149 n n C3' H3' DL5 sing 150 n n C3F C4F DL5 sing 151 n n C3F H3F DL5 sing 152 n n O3G HO3G DL5 sing 153 n n C5' C4' DL5 sing 154 n n C4' O4' DL5 sing 155 n n C4' H4' DL5 sing 156 n n N4F C4F DL5 doub 157 n n C4F C5F DL5 sing 158 n n O5F N4F DL5 sing 159 n n N4F O4F DL5 sing 160 n n O5' C5' DL5 sing 161 n n C5' H5' DL5 sing 162 n n C5' "H5'A" DL5 sing 163 n n C5F C6F DL5 doub 164 n n C5F H5F DL5 sing 165 n n C6F N6F DL5 sing 166 n n N6F O7F DL5 sing 167 n n N6F O6F DL5 doub 168 n n H4F O4F DL5 sing 169 n n # _atom_sites.entry_id 5A3R _atom_sites.fract_transf_matrix[1][1] 0.017382 _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] 0.008698 _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] 0.004392 _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 DL5 A 1 1000 1000 DL5 DL5 . C 3 K A 1 1006 1006 K K . D 4 MG A 1 1007 1007 MG MG . E 4 MG A 1 1008 1008 MG MG . F 4 MG A 1 1009 1009 MG MG . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 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 . . . B 2 1.195 0.884 14.112 1 98.83 ? N1 DL5 1000 A 1 HETATM 2 C C2 DL5 . . . B 2 2.491 1.231 13.81 1 99.13 ? C2 DL5 1000 A 1 HETATM 3 N N3 DL5 . . . B 2 2.832 2.535 13.529 1 97.8 ? N3 DL5 1000 A 1 HETATM 4 C C4 DL5 . . . B 2 1.924 3.604 13.523 1 101.26 ? C4 DL5 1000 A 1 HETATM 5 C C5 DL5 . . . B 2 0.599 3.287 13.825 1 104.27 ? C5 DL5 1000 A 1 HETATM 6 C C6 DL5 . . . B 2 0.214 1.928 14.122 1 104.01 ? C6 DL5 1000 A 1 HETATM 7 N N6 DL5 . . . B 2 -1.075 1.654 14.412 1 111.85 ? N6 DL5 1000 A 1 HETATM 8 N N7 DL5 . . . B 2 -0.169 4.382 13.787 1 110.99 ? N7 DL5 1000 A 1 HETATM 9 C C8 DL5 . . . B 2 0.654 5.335 13.474 1 110.09 ? C8 DL5 1000 A 1 HETATM 10 N N9 DL5 . . . B 2 1.948 4.954 13.292 1 110.59 ? N9 DL5 1000 A 1 HETATM 11 P PA DL5 . . . B 2 -0.574 7.765 10.282 1 112.94 ? PA DL5 1000 A 1 HETATM 12 P PB DL5 . . . B 2 -2.968 6.55 11.768 1 133.26 ? PB DL5 1000 A 1 HETATM 13 P PG DL5 . . . B 2 -4.091 3.721 11.81 1 148.17 ? PG DL5 1000 A 1 HETATM 14 C C01 DL5 . . . B 2 -3.292 5.029 12.692 1 141.42 ? C01 DL5 1000 A 1 HETATM 15 C C1' DL5 . . . B 2 3.188 5.727 12.932 1 101.93 ? C1' DL5 1000 A 1 HETATM 16 O O1A DL5 . . . B 2 0.203 7.467 8.934 1 131.57 ? O1A DL5 1000 A 1 HETATM 17 O O1B DL5 . . . B 2 -2.68 7.591 12.686 1 143.89 ? O1B DL5 1000 A 1 HETATM 18 C C1F DL5 . . . B 2 5.751 6.406 10.764 1 98.82 ? C1F DL5 1000 A 1 HETATM 19 O O1G DL5 . . . B 2 -5.034 4.227 10.622 1 139.89 ? O1G DL5 1000 A 1 HETATM 20 C C2' DL5 . . . B 2 3.649 5.665 11.444 1 97.38 ? C2' DL5 1000 A 1 HETATM 21 O O2' DL5 . . . B 2 5.027 5.196 11.389 1 96.35 ? O2' DL5 1000 A 1 HETATM 22 O O2A DL5 . . . B 2 -1.471 8.984 10.25 1 102.77 ? O2A DL5 1000 A 1 HETATM 23 O O2B DL5 . . . B 2 -4.154 6.853 11.113 1 138.56 ? O2B DL5 1000 A 1 HETATM 24 C C2F DL5 . . . B 2 6.441 5.804 9.497 1 102.02 ? C2F DL5 1000 A 1 HETATM 25 N N2F DL5 . . . B 2 5.714 5.181 8.402 1 98.9 ? N2F DL5 1000 A 1 HETATM 26 O O2F DL5 . . . B 2 6.237 4.713 7.435 1 106.78 ? O2F DL5 1000 A 1 HETATM 27 O O2G DL5 . . . B 2 -5.045 3.02 12.883 1 154.5 ? O2G DL5 1000 A 1 HETATM 28 C C3' DL5 . . . B 2 3.516 7.137 10.849 1 101.01 ? C3' DL5 1000 A 1 HETATM 29 O O3' DL5 . . . B 2 4.839 7.59 10.44 1 98.71 ? O3' DL5 1000 A 1 HETATM 30 O O3A DL5 . . . B 2 -1.592 6.58 10.743 1 114.55 ? O3A DL5 1000 A 1 HETATM 31 C C3F DL5 . . . B 2 7.845 5.825 9.349 1 107.2 ? C3F DL5 1000 A 1 HETATM 32 O O3F DL5 . . . B 2 4.493 5.093 8.398 1 100.38 ? O3F DL5 1000 A 1 HETATM 33 O O3G DL5 . . . B 2 -3.201 2.727 11.237 1 150.02 ? O3G DL5 1000 A 1 HETATM 34 C C4' DL5 . . . B 2 3.008 8.044 11.857 1 96.62 ? C4' DL5 1000 A 1 HETATM 35 O O4' DL5 . . . B 2 2.874 7.086 12.981 1 81.67 ? O4' DL5 1000 A 1 HETATM 36 C C4F DL5 . . . B 2 8.789 6.348 10.226 1 112.98 ? C4F DL5 1000 A 1 HETATM 37 N N4F DL5 . . . B 2 10.121 6.347 10.047 1 126.61 ? N4F DL5 1000 A 1 HETATM 38 O O4F DL5 . . . B 2 10.919 6.821 10.849 1 126.94 ? O4F DL5 1000 A 1 HETATM 39 C C5' DL5 . . . B 2 1.536 8.705 11.747 1 101.92 ? C5' DL5 1000 A 1 HETATM 40 O O5' DL5 . . . B 2 0.538 7.674 11.518 1 108.63 ? O5' DL5 1000 A 1 HETATM 41 C C5F DL5 . . . B 2 8.264 6.929 11.411 1 111.08 ? C5F DL5 1000 A 1 HETATM 42 O O5F DL5 . . . B 2 10.632 5.865 9.055 1 132.14 ? O5F DL5 1000 A 1 HETATM 43 C C6F DL5 . . . B 2 6.799 7.019 11.765 1 107.18 ? C6F DL5 1000 A 1 HETATM 44 N N6F DL5 . . . B 2 6.592 7.676 13.067 1 114.24 ? N6F DL5 1000 A 1 HETATM 45 O O6F DL5 . . . B 2 7.575 8.085 13.72 1 116.61 ? O6F DL5 1000 A 1 HETATM 46 O O7F DL5 . . . B 2 5.559 7.883 13.603 1 120.34 ? O7F DL5 1000 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #