data_3D5I # _model_server_result.job_id nUiJjcA0BFn6-OT9b630jA _model_server_result.datetime_utc '2024-10-15 04:36:22' _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 3d5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":98}' # _entry.id 3D5I # _exptl.entry_id 3D5I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 361.271 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE" _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 100.8 _cell.angle_gamma 90 _cell.entry_id 3D5I _cell.length_a 101.221 _cell.length_b 66.775 _cell.length_c 57.07 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,H 1 1 B,F,I 2 1 C,G,J 3 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 3 _struct_asym.id F _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 9 A CYS 9 1_555 A SG CYS 97 A CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf2 B SG CYS 9 B CYS 9 1_555 B SG CYS 97 B CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 C SG CYS 9 C CYS 9 1_555 C SG CYS 97 C CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C10 H12 N5 O6 P S' _chem_comp.formula_weight 361.271 _chem_comp.id SGP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE" _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 P S1P SGP doub 271 n n P O1P SGP sing 272 n n P O3' SGP sing 273 n n P O2' SGP sing 274 n n O1P HOP1 SGP sing 275 n n O5' C5' SGP sing 276 n n O5' HO5' SGP sing 277 n n C5' C4' SGP sing 278 n n C5' "H5'1" SGP sing 279 n n C5' "H5'2" SGP sing 280 n n C4' O4' SGP sing 281 n n C4' C3' SGP sing 282 n n C4' H4' SGP sing 283 n n O4' C1' SGP sing 284 n n C3' O3' SGP sing 285 n n C3' C2' SGP sing 286 n n C3' H3' SGP sing 287 n n C2' O2' SGP sing 288 n n C2' C1' SGP sing 289 n n C2' H2' SGP sing 290 n n C1' N9 SGP sing 291 n n C1' H1' SGP sing 292 n n N9 C8 SGP sing 293 n y N9 C4 SGP sing 294 n y C8 N7 SGP doub 295 n y C8 H8 SGP sing 296 n n N7 C5 SGP sing 297 n y C5 C6 SGP sing 298 n n C5 C4 SGP doub 299 n y C6 O6 SGP doub 300 n n C6 N1 SGP sing 301 n n N1 C2 SGP sing 302 n n N1 HN1 SGP sing 303 n n C2 N2 SGP sing 304 n n C2 N3 SGP doub 305 n n N2 HN21 SGP sing 306 n n N2 HN22 SGP sing 307 n n N3 C4 SGP sing 308 n n # _atom_sites.entry_id 3D5I _atom_sites.fract_transf_matrix[1][1] 0.009879 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001884 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014976 _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] 0.017838 _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 D 2 SO4 A 1 98 98 SO4 SO4 . E 2 SO4 A 1 99 99 SO4 SO4 . F 3 SGP B 1 98 98 SGP SGP . G 2 SO4 C 1 98 98 SO4 SO4 . H 4 HOH A 1 100 6 HOH HOH . H 4 HOH A 2 101 7 HOH HOH . H 4 HOH A 3 102 8 HOH HOH . H 4 HOH A 4 103 13 HOH HOH . H 4 HOH A 5 104 15 HOH HOH . H 4 HOH A 6 105 16 HOH HOH . H 4 HOH A 7 106 20 HOH HOH . H 4 HOH A 8 107 22 HOH HOH . H 4 HOH A 9 108 26 HOH HOH . H 4 HOH A 10 109 27 HOH HOH . H 4 HOH A 11 110 28 HOH HOH . H 4 HOH A 12 111 32 HOH HOH . H 4 HOH A 13 112 36 HOH HOH . H 4 HOH A 14 113 39 HOH HOH . H 4 HOH A 15 114 41 HOH HOH . H 4 HOH A 16 115 42 HOH HOH . H 4 HOH A 17 116 46 HOH HOH . H 4 HOH A 18 117 49 HOH HOH . H 4 HOH A 19 118 52 HOH HOH . H 4 HOH A 20 119 57 HOH HOH . H 4 HOH A 21 120 59 HOH HOH . H 4 HOH A 22 121 60 HOH HOH . H 4 HOH A 23 122 61 HOH HOH . H 4 HOH A 24 123 63 HOH HOH . H 4 HOH A 25 124 70 HOH HOH . H 4 HOH A 26 125 72 HOH HOH . H 4 HOH A 27 126 76 HOH HOH . H 4 HOH A 28 127 77 HOH HOH . H 4 HOH A 29 128 80 HOH HOH . H 4 HOH A 30 129 81 HOH HOH . H 4 HOH A 31 130 83 HOH HOH . H 4 HOH A 32 131 84 HOH HOH . H 4 HOH A 33 132 86 HOH HOH . H 4 HOH A 34 133 88 HOH HOH . H 4 HOH A 35 134 93 HOH HOH . H 4 HOH A 36 135 94 HOH HOH . H 4 HOH A 37 136 95 HOH HOH . H 4 HOH A 38 137 97 HOH HOH . H 4 HOH A 39 138 99 HOH HOH . H 4 HOH A 40 139 100 HOH HOH . H 4 HOH A 41 140 101 HOH HOH . H 4 HOH A 42 141 102 HOH HOH . H 4 HOH A 43 142 103 HOH HOH . H 4 HOH A 44 143 107 HOH HOH . H 4 HOH A 45 144 110 HOH HOH . H 4 HOH A 46 145 112 HOH HOH . H 4 HOH A 47 146 114 HOH HOH . H 4 HOH A 48 147 118 HOH HOH . H 4 HOH A 49 148 119 HOH HOH . H 4 HOH A 50 149 121 HOH HOH . H 4 HOH A 51 150 122 HOH HOH . H 4 HOH A 52 151 125 HOH HOH . H 4 HOH A 53 152 129 HOH HOH . H 4 HOH A 54 153 139 HOH HOH . H 4 HOH A 55 154 140 HOH HOH . H 4 HOH A 56 155 142 HOH HOH . H 4 HOH A 57 156 144 HOH HOH . H 4 HOH A 58 157 145 HOH HOH . H 4 HOH A 59 158 146 HOH HOH . H 4 HOH A 60 159 147 HOH HOH . H 4 HOH A 61 160 148 HOH HOH . H 4 HOH A 62 161 150 HOH HOH . H 4 HOH A 63 162 152 HOH HOH . H 4 HOH A 64 163 154 HOH HOH . H 4 HOH A 65 164 162 HOH HOH . H 4 HOH A 66 165 164 HOH HOH . H 4 HOH A 67 166 166 HOH HOH . H 4 HOH A 68 167 172 HOH HOH . H 4 HOH A 69 168 179 HOH HOH . H 4 HOH A 70 169 182 HOH HOH . H 4 HOH A 71 170 192 HOH HOH . H 4 HOH A 72 171 193 HOH HOH . H 4 HOH A 73 172 23 HOH HOH . H 4 HOH A 74 173 25 HOH HOH . I 4 HOH B 1 114 40 HOH HOH . I 4 HOH B 2 115 113 HOH HOH . I 4 HOH B 3 116 3 HOH HOH . I 4 HOH B 4 117 5 HOH HOH . I 4 HOH B 5 118 9 HOH HOH . I 4 HOH B 6 119 11 HOH HOH . I 4 HOH B 7 120 12 HOH HOH . I 4 HOH B 8 121 14 HOH HOH . I 4 HOH B 9 122 17 HOH HOH . I 4 HOH B 10 123 18 HOH HOH . I 4 HOH B 11 124 24 HOH HOH . I 4 HOH B 12 125 30 HOH HOH . I 4 HOH B 13 126 31 HOH HOH . I 4 HOH B 14 127 33 HOH HOH . I 4 HOH B 15 128 38 HOH HOH . I 4 HOH B 16 129 43 HOH HOH . I 4 HOH B 17 130 44 HOH HOH . I 4 HOH B 18 131 47 HOH HOH . I 4 HOH B 19 132 50 HOH HOH . I 4 HOH B 20 133 51 HOH HOH . I 4 HOH B 21 134 54 HOH HOH . I 4 HOH B 22 135 66 HOH HOH . I 4 HOH B 23 136 67 HOH HOH . I 4 HOH B 24 137 68 HOH HOH . I 4 HOH B 25 138 87 HOH HOH . I 4 HOH B 26 139 98 HOH HOH . I 4 HOH B 27 140 105 HOH HOH . I 4 HOH B 28 141 106 HOH HOH . I 4 HOH B 29 142 108 HOH HOH . I 4 HOH B 30 143 116 HOH HOH . I 4 HOH B 31 144 120 HOH HOH . I 4 HOH B 32 145 126 HOH HOH . I 4 HOH B 33 146 127 HOH HOH . I 4 HOH B 34 147 132 HOH HOH . I 4 HOH B 35 148 134 HOH HOH . I 4 HOH B 36 149 136 HOH HOH . I 4 HOH B 37 150 137 HOH HOH . I 4 HOH B 38 151 138 HOH HOH . I 4 HOH B 39 152 143 HOH HOH . I 4 HOH B 40 153 149 HOH HOH . I 4 HOH B 41 154 151 HOH HOH . I 4 HOH B 42 155 159 HOH HOH . I 4 HOH B 43 156 160 HOH HOH . I 4 HOH B 44 157 161 HOH HOH . I 4 HOH B 45 158 169 HOH HOH . I 4 HOH B 46 159 170 HOH HOH . I 4 HOH B 47 160 188 HOH HOH . I 4 HOH B 48 161 194 HOH HOH . I 4 HOH B 49 162 195 HOH HOH . I 4 HOH B 50 163 196 HOH HOH . J 4 HOH C 1 99 10 HOH HOH . J 4 HOH C 2 100 19 HOH HOH . J 4 HOH C 3 101 21 HOH HOH . J 4 HOH C 4 104 29 HOH HOH . J 4 HOH C 5 105 34 HOH HOH . J 4 HOH C 6 106 35 HOH HOH . J 4 HOH C 7 107 37 HOH HOH . J 4 HOH C 8 108 45 HOH HOH . J 4 HOH C 9 109 48 HOH HOH . J 4 HOH C 10 110 53 HOH HOH . J 4 HOH C 11 111 55 HOH HOH . J 4 HOH C 12 112 56 HOH HOH . J 4 HOH C 13 113 58 HOH HOH . J 4 HOH C 14 114 62 HOH HOH . J 4 HOH C 15 115 64 HOH HOH . J 4 HOH C 16 116 65 HOH HOH . J 4 HOH C 17 117 69 HOH HOH . J 4 HOH C 18 118 71 HOH HOH . J 4 HOH C 19 119 74 HOH HOH . J 4 HOH C 20 120 75 HOH HOH . J 4 HOH C 21 121 78 HOH HOH . J 4 HOH C 22 122 79 HOH HOH . J 4 HOH C 23 123 82 HOH HOH . J 4 HOH C 24 124 85 HOH HOH . J 4 HOH C 25 125 90 HOH HOH . J 4 HOH C 26 126 91 HOH HOH . J 4 HOH C 27 127 92 HOH HOH . J 4 HOH C 28 128 96 HOH HOH . J 4 HOH C 29 129 104 HOH HOH . J 4 HOH C 30 130 109 HOH HOH . J 4 HOH C 31 131 111 HOH HOH . J 4 HOH C 32 132 115 HOH HOH . J 4 HOH C 33 133 117 HOH HOH . J 4 HOH C 34 134 123 HOH HOH . J 4 HOH C 35 135 124 HOH HOH . J 4 HOH C 36 136 128 HOH HOH . J 4 HOH C 37 137 130 HOH HOH . J 4 HOH C 38 138 133 HOH HOH . J 4 HOH C 39 139 135 HOH HOH . J 4 HOH C 40 140 156 HOH HOH . J 4 HOH C 41 141 163 HOH HOH . J 4 HOH C 42 142 175 HOH HOH . J 4 HOH C 43 143 176 HOH HOH . J 4 HOH C 44 144 184 HOH HOH . J 4 HOH C 45 145 186 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 P SGP . . . F 3 58.472 -27.095 28.856 1 58.8 ? P SGP 98 B 1 HETATM 2 S S1P SGP . . . F 3 59.458 -27.505 27.245 1 64.52 ? S1P SGP 98 B 1 HETATM 3 O O1P SGP . . . F 3 56.734 -27.262 28.566 1 59.98 ? O1P SGP 98 B 1 HETATM 4 O O5' SGP . . . F 3 61.65 -28.066 32.764 1 56.59 ? O5' SGP 98 B 1 HETATM 5 C C5' SGP . . . F 3 60.278 -27.81 33.105 1 56.09 ? C5' SGP 98 B 1 HETATM 6 C C4' SGP . . . F 3 59.678 -26.748 32.186 1 54.72 ? C4' SGP 98 B 1 HETATM 7 O O4' SGP . . . F 3 60.178 -25.419 32.399 1 52.27 ? O4' SGP 98 B 1 HETATM 8 C C3' SGP . . . F 3 60.035 -27.071 30.761 1 55.6 ? C3' SGP 98 B 1 HETATM 9 O O3' SGP . . . F 3 59.037 -27.873 30.128 1 57.79 ? O3' SGP 98 B 1 HETATM 10 C C2' SGP . . . F 3 60.138 -25.714 30.088 1 53.48 ? C2' SGP 98 B 1 HETATM 11 O O2' SGP . . . F 3 58.942 -25.628 29.327 1 56.91 ? O2' SGP 98 B 1 HETATM 12 C C1' SGP . . . F 3 60.241 -24.667 31.17 1 47.11 ? C1' SGP 98 B 1 HETATM 13 N N9 SGP . . . F 3 61.502 -23.859 31.204 1 45.32 ? N9 SGP 98 B 1 HETATM 14 C C8 SGP . . . F 3 61.554 -22.503 31.292 1 44.32 ? C8 SGP 98 B 1 HETATM 15 N N7 SGP . . . F 3 62.841 -22.059 31.373 1 43.82 ? N7 SGP 98 B 1 HETATM 16 C C5 SGP . . . F 3 63.638 -23.138 31.346 1 43.72 ? C5 SGP 98 B 1 HETATM 17 C C6 SGP . . . F 3 65.097 -23.385 31.389 1 44.07 ? C6 SGP 98 B 1 HETATM 18 O O6 SGP . . . F 3 65.903 -22.439 31.483 1 43.51 ? O6 SGP 98 B 1 HETATM 19 N N1 SGP . . . F 3 65.518 -24.668 31.336 1 44.19 ? N1 SGP 98 B 1 HETATM 20 C C2 SGP . . . F 3 64.658 -25.703 31.258 1 43.48 ? C2 SGP 98 B 1 HETATM 21 N N2 SGP . . . F 3 65.151 -26.962 31.217 1 45.04 ? N2 SGP 98 B 1 HETATM 22 N N3 SGP . . . F 3 63.319 -25.554 31.213 1 42.41 ? N3 SGP 98 B 1 HETATM 23 C C4 SGP . . . F 3 62.757 -24.323 31.252 1 43.94 ? C4 SGP 98 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 23 #