data_1RPF # _model_server_result.job_id SgJ2hjqhMC7CeT5Sog5uHA _model_server_result.datetime_utc '2024-11-25 05:33:12' _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 1rpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":125}' # _entry.id 1RPF # _exptl.entry_id 1RPF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-3'-MONOPHOSPHATE" _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 120 _cell.entry_id 1RPF _cell.length_a 65.25 _cell.length_b 65.25 _cell.length_c 65.52 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C3P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-3'-MONOPHOSPHATE" _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 O1P C3P doub 70 n n P O2P C3P sing 71 n n P O3P C3P sing 72 n n P O3' C3P sing 73 n n O2P HOP2 C3P sing 74 n n O3P HOP3 C3P sing 75 n n O5' C5' C3P sing 76 n n O5' HO5' C3P sing 77 n n C5' C4' C3P sing 78 n n C5' "H5'1" C3P sing 79 n n C5' "H5'2" C3P sing 80 n n C4' O4' C3P sing 81 n n C4' C3' C3P sing 82 n n C4' H4' C3P sing 83 n n O4' C1' C3P sing 84 n n C3' O3' C3P sing 85 n n C3' C2' C3P sing 86 n n C3' H3' C3P sing 87 n n C2' O2' C3P sing 88 n n C2' C1' C3P sing 89 n n C2' "H2'1" C3P sing 90 n n O2' HO2' C3P sing 91 n n C1' N1 C3P sing 92 n n C1' H1' C3P sing 93 n n N1 C2 C3P sing 94 n n N1 C6 C3P sing 95 n n C2 N3 C3P sing 96 n n C2 O2 C3P doub 97 n n N3 C4 C3P doub 98 n n C4 C5 C3P sing 99 n n C4 N4 C3P sing 100 n n C5 C6 C3P doub 101 n n C5 H5 C3P sing 102 n n C6 H6 C3P sing 103 n n N4 HN41 C3P sing 104 n n N4 HN42 C3P sing 105 n n # _atom_sites.entry_id 1RPF _atom_sites.fract_transf_matrix[1][1] 0.015326 _atom_sites.fract_transf_matrix[1][2] 0.008848 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017697 _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] 0.015263 _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 C3P A 1 125 125 C3P C3P . C 3 HOH A 1 126 126 HOH HOH . C 3 HOH A 2 127 127 HOH HOH . C 3 HOH A 3 128 128 HOH HOH . C 3 HOH A 4 129 129 HOH HOH . C 3 HOH A 5 130 130 HOH HOH . C 3 HOH A 6 131 131 HOH HOH . C 3 HOH A 7 132 132 HOH HOH . C 3 HOH A 8 133 133 HOH HOH . C 3 HOH A 9 134 134 HOH HOH . C 3 HOH A 10 135 135 HOH HOH . C 3 HOH A 11 136 136 HOH HOH . C 3 HOH A 12 137 137 HOH HOH . C 3 HOH A 13 138 138 HOH HOH . C 3 HOH A 14 139 139 HOH HOH . C 3 HOH A 15 140 140 HOH HOH . C 3 HOH A 16 141 141 HOH HOH . C 3 HOH A 17 142 142 HOH HOH . C 3 HOH A 18 143 143 HOH HOH . C 3 HOH A 19 144 144 HOH HOH . C 3 HOH A 20 145 145 HOH HOH . C 3 HOH A 21 146 146 HOH HOH . C 3 HOH A 22 147 147 HOH HOH . C 3 HOH A 23 148 148 HOH HOH . C 3 HOH A 24 149 149 HOH HOH . C 3 HOH A 25 150 150 HOH HOH . C 3 HOH A 26 151 151 HOH HOH . C 3 HOH A 27 152 152 HOH HOH . C 3 HOH A 28 153 153 HOH HOH . C 3 HOH A 29 154 154 HOH HOH . C 3 HOH A 30 155 155 HOH HOH . C 3 HOH A 31 156 156 HOH HOH . C 3 HOH A 32 157 157 HOH HOH . C 3 HOH A 33 158 158 HOH HOH . C 3 HOH A 34 159 159 HOH HOH . C 3 HOH A 35 160 160 HOH HOH . C 3 HOH A 36 161 161 HOH HOH . C 3 HOH A 37 162 162 HOH HOH . C 3 HOH A 38 163 163 HOH HOH . C 3 HOH A 39 164 164 HOH HOH . C 3 HOH A 40 165 165 HOH HOH . C 3 HOH A 41 166 166 HOH HOH . C 3 HOH A 42 167 167 HOH HOH . C 3 HOH A 43 168 168 HOH HOH . C 3 HOH A 44 170 170 HOH HOH . C 3 HOH A 45 171 171 HOH HOH . C 3 HOH A 46 172 172 HOH HOH . C 3 HOH A 47 173 173 HOH HOH . C 3 HOH A 48 174 174 HOH HOH . C 3 HOH A 49 175 175 HOH HOH . C 3 HOH A 50 176 176 HOH HOH . C 3 HOH A 51 177 177 HOH HOH . C 3 HOH A 52 178 178 HOH HOH . C 3 HOH A 53 179 179 HOH HOH . C 3 HOH A 54 180 180 HOH HOH . C 3 HOH A 55 181 181 HOH HOH . C 3 HOH A 56 182 182 HOH HOH . C 3 HOH A 57 183 183 HOH HOH . C 3 HOH A 58 184 184 HOH HOH . C 3 HOH A 59 185 185 HOH HOH . C 3 HOH A 60 186 186 HOH HOH . C 3 HOH A 61 187 187 HOH HOH . C 3 HOH A 62 188 188 HOH HOH . C 3 HOH A 63 189 189 HOH HOH . C 3 HOH A 64 190 190 HOH HOH . C 3 HOH A 65 191 191 HOH HOH . C 3 HOH A 66 192 192 HOH HOH . C 3 HOH A 67 193 193 HOH HOH . C 3 HOH A 68 194 194 HOH HOH . C 3 HOH A 69 195 195 HOH HOH . C 3 HOH A 70 196 196 HOH HOH . C 3 HOH A 71 197 197 HOH HOH . C 3 HOH A 72 198 198 HOH HOH . C 3 HOH A 73 199 199 HOH HOH . C 3 HOH A 74 200 200 HOH HOH . C 3 HOH A 75 201 201 HOH HOH . C 3 HOH A 76 202 202 HOH HOH . C 3 HOH A 77 203 203 HOH HOH . C 3 HOH A 78 204 204 HOH HOH . C 3 HOH A 79 205 205 HOH HOH . C 3 HOH A 80 206 206 HOH HOH . C 3 HOH A 81 207 207 HOH HOH . C 3 HOH A 82 208 208 HOH HOH . C 3 HOH A 83 209 209 HOH HOH . C 3 HOH A 84 210 210 HOH HOH . C 3 HOH A 85 211 211 HOH HOH . C 3 HOH A 86 212 212 HOH HOH . C 3 HOH A 87 213 213 HOH HOH . C 3 HOH A 88 214 214 HOH HOH . C 3 HOH A 89 215 215 HOH HOH . C 3 HOH A 90 216 216 HOH HOH . C 3 HOH A 91 217 217 HOH HOH . C 3 HOH A 92 218 218 HOH HOH . C 3 HOH A 93 219 219 HOH HOH . C 3 HOH A 94 220 220 HOH HOH . C 3 HOH A 95 221 221 HOH HOH . C 3 HOH A 96 222 222 HOH HOH . C 3 HOH A 97 223 223 HOH HOH . C 3 HOH A 98 224 224 HOH HOH . C 3 HOH A 99 225 225 HOH HOH . C 3 HOH A 100 226 226 HOH HOH . C 3 HOH A 101 227 227 HOH HOH . C 3 HOH A 102 228 228 HOH HOH . C 3 HOH A 103 229 229 HOH HOH . C 3 HOH A 104 230 230 HOH HOH . C 3 HOH A 105 231 231 HOH HOH . C 3 HOH A 106 232 232 HOH HOH . C 3 HOH A 107 233 233 HOH HOH . C 3 HOH A 108 234 234 HOH HOH . C 3 HOH A 109 235 235 HOH HOH . C 3 HOH A 110 236 236 HOH HOH . C 3 HOH A 111 237 237 HOH HOH . C 3 HOH A 112 238 238 HOH HOH . C 3 HOH A 113 239 239 HOH HOH . C 3 HOH A 114 240 240 HOH HOH . C 3 HOH A 115 241 241 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 C3P . . . B 2 -13.007 47.578 6.678 1 0.4 ? P C3P 125 A 1 HETATM 2 O O1P C3P . . . B 2 -12.495 47.755 8.066 1 0.71 ? O1P C3P 125 A 1 HETATM 3 O O2P C3P . . . B 2 -11.909 46.966 5.845 1 0.45 ? O2P C3P 125 A 1 HETATM 4 O O3P C3P . . . B 2 -14.292 46.843 6.513 1 0.66 ? O3P C3P 125 A 1 HETATM 5 O O5' C3P . . . B 2 -14.672 52.951 6.555 1 1.39 ? O5' C3P 125 A 1 HETATM 6 C C5' C3P . . . B 2 -13.624 52.123 7.034 1 0.44 ? C5' C3P 125 A 1 HETATM 7 C C4' C3P . . . B 2 -12.94 51.438 5.823 1 0.33 ? C4' C3P 125 A 1 HETATM 8 O O4' C3P . . . B 2 -11.881 52.123 5.071 1 0.37 ? O4' C3P 125 A 1 HETATM 9 C C3' C3P . . . B 2 -12.385 50.076 6.114 1 0.3 ? C3' C3P 125 A 1 HETATM 10 O O3' C3P . . . B 2 -13.3 49.035 6.062 1 0.51 ? O3' C3P 125 A 1 HETATM 11 C C2' C3P . . . B 2 -11.198 49.911 5.169 1 0.34 ? C2' C3P 125 A 1 HETATM 12 O O2' C3P . . . B 2 -11.347 48.779 4.286 1 0.55 ? O2' C3P 125 A 1 HETATM 13 C C1' C3P . . . B 2 -10.733 51.309 4.911 1 0.41 ? C1' C3P 125 A 1 HETATM 14 N N1 C3P . . . B 2 -9.685 51.84 5.735 1 0.39 ? N1 C3P 125 A 1 HETATM 15 C C2 C3P . . . B 2 -8.441 51.398 5.523 1 0.19 ? C2 C3P 125 A 1 HETATM 16 N N3 C3P . . . B 2 -7.435 51.961 6.211 1 0.27 ? N3 C3P 125 A 1 HETATM 17 C C4 C3P . . . B 2 -7.666 52.898 7.128 1 0.48 ? C4 C3P 125 A 1 HETATM 18 C C5 C3P . . . B 2 -8.971 53.33 7.365 1 0.31 ? C5 C3P 125 A 1 HETATM 19 C C6 C3P . . . B 2 -9.942 52.824 6.643 1 0.38 ? C6 C3P 125 A 1 HETATM 20 O O2 C3P . . . B 2 -8.287 50.525 4.7 1 0.27 ? O2 C3P 125 A 1 HETATM 21 N N4 C3P . . . B 2 -6.724 53.496 7.843 1 0.23 ? N4 C3P 125 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #