data_3SBD # _model_server_result.job_id 7W27qNLo9FfVFcENi_wINA _model_server_result.datetime_utc '2024-10-12 15:28:51' _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 3sbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 3SBD # _exptl.entry_id 3SBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 3SBD _cell.length_a 50.266 _cell.length_b 80.021 _cell.length_c 94.91 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 27 A THR 17 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 A OG1 THR 45 A THR 35 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc3 G O HOH . A HOH 233 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc4 G O HOH . A HOH 234 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc5 C O2G GNP . A GNP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc6 C O2B GNP . A GNP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc7 B OG1 THR 27 B THR 17 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc8 B OG1 THR 45 B THR 35 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc9 H O HOH . B HOH 235 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc10 H O HOH . B HOH 236 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc11 E O3G GNP . B GNP 502 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc12 E O2B GNP . B GNP 502 1_555 F MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 3SBD _atom_sites.fract_transf_matrix[1][1] 0.019894 _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] 0.012497 _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] 0.010536 _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 2 GNP A 1 500 500 GNP GNP . D 3 MG A 1 501 501 MG MG . E 2 GNP B 1 502 502 GNP GNP . F 3 MG B 1 503 503 MG MG . G 4 HOH A 1 178 1 HOH HOH . G 4 HOH A 2 179 3 HOH HOH . G 4 HOH A 3 180 4 HOH HOH . G 4 HOH A 4 181 9 HOH HOH . G 4 HOH A 5 182 13 HOH HOH . G 4 HOH A 6 183 14 HOH HOH . G 4 HOH A 7 184 15 HOH HOH . G 4 HOH A 8 185 16 HOH HOH . G 4 HOH A 9 186 20 HOH HOH . G 4 HOH A 10 187 21 HOH HOH . G 4 HOH A 11 188 23 HOH HOH . G 4 HOH A 12 189 24 HOH HOH . G 4 HOH A 13 190 26 HOH HOH . G 4 HOH A 14 191 28 HOH HOH . G 4 HOH A 15 192 31 HOH HOH . G 4 HOH A 16 193 33 HOH HOH . G 4 HOH A 17 194 35 HOH HOH . G 4 HOH A 18 195 36 HOH HOH . G 4 HOH A 19 196 37 HOH HOH . G 4 HOH A 20 197 42 HOH HOH . G 4 HOH A 21 198 45 HOH HOH . G 4 HOH A 22 199 46 HOH HOH . G 4 HOH A 23 200 47 HOH HOH . G 4 HOH A 24 201 48 HOH HOH . G 4 HOH A 25 202 49 HOH HOH . G 4 HOH A 26 203 53 HOH HOH . G 4 HOH A 27 204 57 HOH HOH . G 4 HOH A 28 205 58 HOH HOH . G 4 HOH A 29 206 60 HOH HOH . G 4 HOH A 30 207 61 HOH HOH . G 4 HOH A 31 208 63 HOH HOH . G 4 HOH A 32 209 64 HOH HOH . G 4 HOH A 33 210 65 HOH HOH . G 4 HOH A 34 211 66 HOH HOH . G 4 HOH A 35 212 68 HOH HOH . G 4 HOH A 36 213 69 HOH HOH . G 4 HOH A 37 214 71 HOH HOH . G 4 HOH A 38 215 72 HOH HOH . G 4 HOH A 39 216 73 HOH HOH . G 4 HOH A 40 217 75 HOH HOH . G 4 HOH A 41 218 76 HOH HOH . G 4 HOH A 42 219 78 HOH HOH . G 4 HOH A 43 220 84 HOH HOH . G 4 HOH A 44 221 87 HOH HOH . G 4 HOH A 45 222 91 HOH HOH . G 4 HOH A 46 223 92 HOH HOH . G 4 HOH A 47 224 95 HOH HOH . G 4 HOH A 48 225 96 HOH HOH . G 4 HOH A 49 226 97 HOH HOH . G 4 HOH A 50 227 98 HOH HOH . G 4 HOH A 51 228 99 HOH HOH . G 4 HOH A 52 229 100 HOH HOH . G 4 HOH A 53 230 105 HOH HOH . G 4 HOH A 54 231 106 HOH HOH . G 4 HOH A 55 232 107 HOH HOH . G 4 HOH A 56 233 112 HOH HOH . G 4 HOH A 57 234 113 HOH HOH . G 4 HOH A 58 235 114 HOH HOH . G 4 HOH A 59 236 115 HOH HOH . G 4 HOH A 60 237 116 HOH HOH . G 4 HOH A 61 238 117 HOH HOH . G 4 HOH A 62 239 118 HOH HOH . G 4 HOH A 63 240 119 HOH HOH . G 4 HOH A 64 241 120 HOH HOH . G 4 HOH A 65 242 121 HOH HOH . G 4 HOH A 66 243 122 HOH HOH . G 4 HOH A 67 244 141 HOH HOH . G 4 HOH A 68 245 144 HOH HOH . G 4 HOH A 69 246 145 HOH HOH . G 4 HOH A 70 247 146 HOH HOH . H 4 HOH B 1 178 2 HOH HOH . H 4 HOH B 2 179 5 HOH HOH . H 4 HOH B 3 180 6 HOH HOH . H 4 HOH B 4 181 7 HOH HOH . H 4 HOH B 5 182 8 HOH HOH . H 4 HOH B 6 183 10 HOH HOH . H 4 HOH B 7 184 11 HOH HOH . H 4 HOH B 8 185 12 HOH HOH . H 4 HOH B 9 186 17 HOH HOH . H 4 HOH B 10 187 18 HOH HOH . H 4 HOH B 11 188 19 HOH HOH . H 4 HOH B 12 189 22 HOH HOH . H 4 HOH B 13 190 25 HOH HOH . H 4 HOH B 14 191 27 HOH HOH . H 4 HOH B 15 192 29 HOH HOH . H 4 HOH B 16 193 30 HOH HOH . H 4 HOH B 17 194 32 HOH HOH . H 4 HOH B 18 195 34 HOH HOH . H 4 HOH B 19 196 38 HOH HOH . H 4 HOH B 20 197 39 HOH HOH . H 4 HOH B 21 198 40 HOH HOH . H 4 HOH B 22 199 41 HOH HOH . H 4 HOH B 23 200 43 HOH HOH . H 4 HOH B 24 201 44 HOH HOH . H 4 HOH B 25 202 50 HOH HOH . H 4 HOH B 26 203 51 HOH HOH . H 4 HOH B 27 204 52 HOH HOH . H 4 HOH B 28 205 54 HOH HOH . H 4 HOH B 29 206 55 HOH HOH . H 4 HOH B 30 207 56 HOH HOH . H 4 HOH B 31 208 59 HOH HOH . H 4 HOH B 32 209 62 HOH HOH . H 4 HOH B 33 210 67 HOH HOH . H 4 HOH B 34 211 70 HOH HOH . H 4 HOH B 35 212 74 HOH HOH . H 4 HOH B 36 213 77 HOH HOH . H 4 HOH B 37 214 79 HOH HOH . H 4 HOH B 38 215 80 HOH HOH . H 4 HOH B 39 216 81 HOH HOH . H 4 HOH B 40 217 82 HOH HOH . H 4 HOH B 41 218 83 HOH HOH . H 4 HOH B 42 219 85 HOH HOH . H 4 HOH B 43 220 86 HOH HOH . H 4 HOH B 44 221 88 HOH HOH . H 4 HOH B 45 222 89 HOH HOH . H 4 HOH B 46 223 90 HOH HOH . H 4 HOH B 47 224 93 HOH HOH . H 4 HOH B 48 225 94 HOH HOH . H 4 HOH B 49 226 101 HOH HOH . H 4 HOH B 50 227 102 HOH HOH . H 4 HOH B 51 228 103 HOH HOH . H 4 HOH B 52 229 104 HOH HOH . H 4 HOH B 53 230 108 HOH HOH . H 4 HOH B 54 231 109 HOH HOH . H 4 HOH B 55 232 110 HOH HOH . H 4 HOH B 56 233 111 HOH HOH . H 4 HOH B 57 234 123 HOH HOH . H 4 HOH B 58 235 124 HOH HOH . H 4 HOH B 59 236 125 HOH HOH . H 4 HOH B 60 237 126 HOH HOH . H 4 HOH B 61 238 127 HOH HOH . H 4 HOH B 62 239 128 HOH HOH . H 4 HOH B 63 240 129 HOH HOH . H 4 HOH B 64 241 130 HOH HOH . H 4 HOH B 65 242 131 HOH HOH . H 4 HOH B 66 243 132 HOH HOH . H 4 HOH B 67 244 133 HOH HOH . H 4 HOH B 68 245 134 HOH HOH . H 4 HOH B 69 246 135 HOH HOH . H 4 HOH B 70 247 136 HOH HOH . H 4 HOH B 71 248 137 HOH HOH . H 4 HOH B 72 249 138 HOH HOH . H 4 HOH B 73 250 139 HOH HOH . H 4 HOH B 74 251 140 HOH HOH . H 4 HOH B 75 252 142 HOH HOH . H 4 HOH B 76 253 143 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 P PG GNP . . . C 2 14.357 72.877 14.649 1 25.54 ? PG GNP 500 A 1 HETATM 2 O O1G GNP . . . C 2 15.338 71.919 14.009 1 27.38 ? O1G GNP 500 A 1 HETATM 3 O O2G GNP . . . C 2 13.752 72.31 15.91 1 23.56 ? O2G GNP 500 A 1 HETATM 4 O O3G GNP . . . C 2 15.088 74.177 14.798 1 22.25 ? O3G GNP 500 A 1 HETATM 5 N N3B GNP . . . C 2 13.151 73.174 13.633 1 23.16 ? N3B GNP 500 A 1 HETATM 6 P PB GNP . . . C 2 12.009 72.162 13.116 1 24.1 ? PB GNP 500 A 1 HETATM 7 O O1B GNP . . . C 2 12.527 71.318 12.022 1 25.28 ? O1B GNP 500 A 1 HETATM 8 O O2B GNP . . . C 2 11.43 71.387 14.243 1 22.07 ? O2B GNP 500 A 1 HETATM 9 O O3A GNP . . . C 2 10.863 73.039 12.525 1 24.73 ? O3A GNP 500 A 1 HETATM 10 P PA GNP . . . C 2 9.499 73.382 13.207 1 25.82 ? PA GNP 500 A 1 HETATM 11 O O1A GNP . . . C 2 8.599 72.204 13.234 1 24.91 ? O1A GNP 500 A 1 HETATM 12 O O2A GNP . . . C 2 9.712 74.056 14.484 1 24.29 ? O2A GNP 500 A 1 HETATM 13 O O5' GNP . . . C 2 8.738 74.41 12.28 1 24.26 ? O5' GNP 500 A 1 HETATM 14 C C5' GNP . . . C 2 9.469 75.493 11.669 1 23.93 ? C5' GNP 500 A 1 HETATM 15 C C4' GNP . . . C 2 8.51 76.473 11.008 1 23.19 ? C4' GNP 500 A 1 HETATM 16 O O4' GNP . . . C 2 7.851 75.898 9.84 1 23.38 ? O4' GNP 500 A 1 HETATM 17 C C3' GNP . . . C 2 7.396 76.966 11.922 1 25.05 ? C3' GNP 500 A 1 HETATM 18 O O3' GNP . . . C 2 7.082 78.351 11.68 1 27.05 ? O3' GNP 500 A 1 HETATM 19 C C2' GNP . . . C 2 6.217 76.115 11.483 1 23.88 ? C2' GNP 500 A 1 HETATM 20 O O2' GNP . . . C 2 4.958 76.707 11.812 1 25.67 ? O2' GNP 500 A 1 HETATM 21 C C1' GNP . . . C 2 6.461 75.93 9.993 1 21.61 ? C1' GNP 500 A 1 HETATM 22 N N9 GNP . . . C 2 5.918 74.667 9.494 1 23.05 ? N9 GNP 500 A 1 HETATM 23 C C8 GNP . . . C 2 6.178 73.381 9.969 1 24.94 ? C8 GNP 500 A 1 HETATM 24 N N7 GNP . . . C 2 5.533 72.439 9.318 1 24.35 ? N7 GNP 500 A 1 HETATM 25 C C5 GNP . . . C 2 4.789 73.159 8.363 1 23.23 ? C5 GNP 500 A 1 HETATM 26 C C6 GNP . . . C 2 3.884 72.711 7.368 1 24.35 ? C6 GNP 500 A 1 HETATM 27 O O6 GNP . . . C 2 3.543 71.544 7.117 1 23.22 ? O6 GNP 500 A 1 HETATM 28 N N1 GNP . . . C 2 3.35 73.769 6.607 1 25.25 ? N1 GNP 500 A 1 HETATM 29 C C2 GNP . . . C 2 3.653 75.108 6.777 1 21.94 ? C2 GNP 500 A 1 HETATM 30 N N2 GNP . . . C 2 3.058 75.984 5.949 1 21.36 ? N2 GNP 500 A 1 HETATM 31 N N3 GNP . . . C 2 4.485 75.532 7.705 1 20.74 ? N3 GNP 500 A 1 HETATM 32 C C4 GNP . . . C 2 5.016 74.518 8.457 1 23.02 ? C4 GNP 500 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #