data_1RNM # _model_server_result.job_id BUrdo2xjlRoByIqwDKp9JQ _model_server_result.datetime_utc '2025-03-06 01:45:12' _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 1rnm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":200}' # _entry.id 1RNM # _exptl.entry_id 1RNM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-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 1RNM _cell.length_a 65.63 _cell.length_b 65.63 _cell.length_c 65.38 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RNM _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 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 PISA dimeric 2 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,B,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 65.38 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 E CYS 26 1_555 A SG CYS 84 E CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 40 E CYS 40 1_555 A SG CYS 95 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? disulf ? disulf3 A SG CYS 58 E CYS 58 1_555 A SG CYS 110 E CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? disulf ? disulf4 A SG CYS 65 E CYS 65 1_555 A SG CYS 72 E CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-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 O3P P C5P sing 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 1RNM _atom_sites.fract_transf_matrix[1][1] 0.015237 _atom_sites.fract_transf_matrix[1][2] 0.008797 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017594 _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] 0.015295 _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 SO4 E 1 125 125 SO4 SO4 . C 2 SO4 E 1 126 126 SO4 SO4 . D 2 SO4 E 1 127 127 SO4 SO4 . E 3 C5P E 1 200 200 C5P C . F 4 HOH E 1 201 201 HOH HOH . F 4 HOH E 2 202 202 HOH HOH . F 4 HOH E 3 203 203 HOH HOH . F 4 HOH E 4 204 204 HOH HOH . F 4 HOH E 5 205 205 HOH HOH . F 4 HOH E 6 206 206 HOH HOH . F 4 HOH E 7 207 207 HOH HOH . F 4 HOH E 8 208 208 HOH HOH . F 4 HOH E 9 209 209 HOH HOH . F 4 HOH E 10 210 210 HOH HOH . F 4 HOH E 11 211 211 HOH HOH . F 4 HOH E 12 212 212 HOH HOH . F 4 HOH E 13 213 213 HOH HOH . F 4 HOH E 14 214 214 HOH HOH . F 4 HOH E 15 215 215 HOH HOH . F 4 HOH E 16 216 216 HOH HOH . F 4 HOH E 17 217 217 HOH HOH . F 4 HOH E 18 218 218 HOH HOH . F 4 HOH E 19 219 219 HOH HOH . F 4 HOH E 20 220 220 HOH HOH . F 4 HOH E 21 221 221 HOH HOH . F 4 HOH E 22 222 222 HOH HOH . F 4 HOH E 23 223 223 HOH HOH . F 4 HOH E 24 224 224 HOH HOH . F 4 HOH E 25 225 225 HOH HOH . F 4 HOH E 26 226 226 HOH HOH . F 4 HOH E 27 227 227 HOH HOH . F 4 HOH E 28 228 228 HOH HOH . F 4 HOH E 29 229 229 HOH HOH . F 4 HOH E 30 230 230 HOH HOH . F 4 HOH E 31 231 231 HOH HOH . F 4 HOH E 32 232 232 HOH HOH . F 4 HOH E 33 233 233 HOH HOH . F 4 HOH E 34 234 234 HOH HOH . F 4 HOH E 35 235 235 HOH HOH . F 4 HOH E 36 236 236 HOH HOH . F 4 HOH E 37 237 237 HOH HOH . F 4 HOH E 38 238 238 HOH HOH . F 4 HOH E 39 239 239 HOH HOH . F 4 HOH E 40 240 240 HOH HOH . F 4 HOH E 41 241 241 HOH HOH . F 4 HOH E 42 242 242 HOH HOH . F 4 HOH E 43 243 243 HOH HOH . F 4 HOH E 44 244 244 HOH HOH . F 4 HOH E 45 245 245 HOH HOH . F 4 HOH E 46 246 246 HOH HOH . F 4 HOH E 47 247 247 HOH HOH . F 4 HOH E 48 248 248 HOH HOH . F 4 HOH E 49 249 249 HOH HOH . F 4 HOH E 50 250 250 HOH HOH . F 4 HOH E 51 251 251 HOH HOH . F 4 HOH E 52 252 252 HOH HOH . F 4 HOH E 53 253 253 HOH HOH . F 4 HOH E 54 254 254 HOH HOH . F 4 HOH E 55 255 255 HOH HOH . F 4 HOH E 56 256 256 HOH HOH . F 4 HOH E 57 257 257 HOH HOH . F 4 HOH E 58 258 258 HOH HOH . F 4 HOH E 59 259 259 HOH HOH . F 4 HOH E 60 260 260 HOH HOH . F 4 HOH E 61 261 261 HOH HOH . F 4 HOH E 62 262 262 HOH HOH . F 4 HOH E 63 263 263 HOH HOH . F 4 HOH E 64 264 264 HOH HOH . F 4 HOH E 65 265 265 HOH HOH . F 4 HOH E 66 266 266 HOH HOH . F 4 HOH E 67 267 267 HOH HOH . F 4 HOH E 68 268 268 HOH HOH . F 4 HOH E 69 269 269 HOH HOH . F 4 HOH E 70 270 270 HOH HOH . F 4 HOH E 71 271 271 HOH HOH . F 4 HOH E 72 272 272 HOH HOH . F 4 HOH E 73 273 273 HOH HOH . F 4 HOH E 74 274 274 HOH HOH . F 4 HOH E 75 275 275 HOH HOH . F 4 HOH E 76 276 276 HOH HOH . F 4 HOH E 77 277 277 HOH HOH . F 4 HOH E 78 278 278 HOH HOH . F 4 HOH E 79 279 279 HOH HOH . F 4 HOH E 80 280 280 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 O O3P C5P . . . E 3 10.24 15.677 29.964 1 64.04 ? O3P C5P 200 E 1 HETATM 2 P P C5P . . . E 3 11.552 15.564 30.696 1 64.41 ? P C5P 200 E 1 HETATM 3 O O1P C5P . . . E 3 11.907 16.712 31.624 1 63.87 ? O1P C5P 200 E 1 HETATM 4 O O2P C5P . . . E 3 11.962 14.183 31.167 1 64.21 ? O2P C5P 200 E 1 HETATM 5 O O5' C5P . . . E 3 12.592 15.706 29.441 1 57.41 ? O5' C5P 200 E 1 HETATM 6 C C5' C5P . . . E 3 12.645 14.728 28.395 1 44.42 ? C5' C5P 200 E 1 HETATM 7 C C4' C5P . . . E 3 13.862 14.961 27.623 1 34.91 ? C4' C5P 200 E 1 HETATM 8 O O4' C5P . . . E 3 14.013 16.314 27.407 1 30.57 ? O4' C5P 200 E 1 HETATM 9 C C3' C5P . . . E 3 15.004 14.575 28.414 1 33.68 ? C3' C5P 200 E 1 HETATM 10 O O3' C5P . . . E 3 15.158 13.25 27.937 1 39.63 ? O3' C5P 200 E 1 HETATM 11 C C2' C5P . . . E 3 16.113 15.518 28.087 1 27.56 ? C2' C5P 200 E 1 HETATM 12 O O2' C5P . . . E 3 16.888 15.052 27.015 1 28.7 ? O2' C5P 200 E 1 HETATM 13 C C1' C5P . . . E 3 15.365 16.621 27.473 1 26.34 ? C1' C5P 200 E 1 HETATM 14 N N1 C5P . . . E 3 15.464 17.894 28.153 1 22.01 ? N1 C5P 200 E 1 HETATM 15 C C2 C5P . . . E 3 16.465 18.718 27.708 1 17.92 ? C2 C5P 200 E 1 HETATM 16 N N3 C5P . . . E 3 16.494 19.94 28.244 1 15.58 ? N3 C5P 200 E 1 HETATM 17 C C4 C5P . . . E 3 15.602 20.361 29.186 1 17.38 ? C4 C5P 200 E 1 HETATM 18 C C5 C5P . . . E 3 14.578 19.508 29.663 1 18.02 ? C5 C5P 200 E 1 HETATM 19 C C6 C5P . . . E 3 14.548 18.286 29.114 1 21.97 ? C6 C5P 200 E 1 HETATM 20 O O2 C5P . . . E 3 17.341 18.36 26.917 1 17.63 ? O2 C5P 200 E 1 HETATM 21 N N4 C5P . . . E 3 15.71 21.583 29.696 1 13.85 ? N4 C5P 200 E 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #