data_9FM3 # _model_server_result.job_id r8Oxmhd1Pi5_CMME6sn56w _model_server_result.datetime_utc '2024-11-15 03:19:28' _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 9fm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 9FM3 # _exptl.entry_id 9FM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.198 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXYCYTIDINE-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 9FM3 _cell.length_a 114.164 _cell.length_b 114.164 _cell.length_c 91.399 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9FM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 6 _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 covale ? covale1 B O3' DA 11 B DA 111 1_555 F P DOC . B DOC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? metalc ? metalc1 A OD1 ASP 318 A ASP 610 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc2 A O TYR 319 A TYR 611 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc3 A OD2 ASP 493 A ASP 785 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc4 D O15 A1IDZ . A A1IDZ 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc5 D O20 A1IDZ . A A1IDZ 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 B DG 101 1_555 C N3 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 B DG 101 1_555 C O2 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 B DG 101 1_555 C N4 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 B DA 102 1_555 C N3 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 B DA 102 1_555 C O4 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 B DC 103 1_555 C N1 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 B DC 103 1_555 C O6 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 B DC 103 1_555 C N2 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 4 B DC 104 1_555 C N1 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 4 B DC 104 1_555 C O6 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 4 B DC 104 1_555 C N2 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 B DA 105 1_555 C N3 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 B DA 105 1_555 C O4 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 106 1_555 C N1 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 106 1_555 C O6 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 106 1_555 C N2 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DG 7 B DG 107 1_555 C N3 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 DG 7 B DG 107 1_555 C O2 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 DG 7 B DG 107 1_555 C N4 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 8 B DG 108 1_555 C N3 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 8 B DG 108 1_555 C O2 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 8 B DG 108 1_555 C N4 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 9 B DC 109 1_555 C N1 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 9 B DC 109 1_555 C O6 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 9 B DC 109 1_555 C N2 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 DC 10 B DC 110 1_555 C N1 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N4 DC 10 B DC 110 1_555 C O6 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O2 DC 10 B DC 110 1_555 C N2 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N1 DA 11 B DA 111 1_555 C N3 DT 6 C DT 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N6 DA 11 B DA 111 1_555 C O4 DT 6 C DT 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N3 O6 P' _chem_comp.formula_weight 291.198 _chem_comp.id DOC _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 N1 C2 DOC sing 234 n n N1 C6 DOC sing 235 n n N1 C1' DOC sing 236 n n C2 N3 DOC sing 237 n n C2 O2 DOC doub 238 n n N3 C4 DOC doub 239 n n C4 C5 DOC sing 240 n n C4 N4 DOC sing 241 n n C5 C6 DOC doub 242 n n C5 H5 DOC sing 243 n n C6 H6 DOC sing 244 n n N4 HN41 DOC sing 245 n n N4 HN42 DOC sing 246 n n C1' C2' DOC sing 247 n n C1' O4' DOC sing 248 n n C1' H1' DOC sing 249 n n C2' C3' DOC sing 250 n n C2' H2' DOC sing 251 n n C2' "H2''" DOC sing 252 n n C3' C4' DOC sing 253 n n C3' "H3'1" DOC sing 254 n n C3' "H3'2" DOC sing 255 n n C4' O4' DOC sing 256 n n C4' C5' DOC sing 257 n n C4' H4' DOC sing 258 n n C5' O5' DOC sing 259 n n C5' H5' DOC sing 260 n n C5' "H5''" DOC sing 261 n n O5' P DOC sing 262 n n P OP1 DOC doub 263 n n P OP2 DOC sing 264 n n P OP3 DOC sing 265 n n OP2 HOP2 DOC sing 266 n n OP3 HOP3 DOC sing 267 n n # _atom_sites.entry_id 9FM3 _atom_sites.fract_transf_matrix[1][1] 0.008759 _atom_sites.fract_transf_matrix[1][2] 0.005057 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010114 _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] 0.010941 _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 4 A1IDZ A 1 901 1 A1IDZ WYZ . E 5 MG A 1 902 1 MG MG . F 6 DOC B 1 201 112 DOC DOC . G 7 HOH A 1 1001 12 HOH HOH . G 7 HOH A 2 1002 11 HOH HOH . G 7 HOH A 3 1003 14 HOH HOH . G 7 HOH A 4 1004 8 HOH HOH . G 7 HOH A 5 1005 6 HOH HOH . G 7 HOH A 6 1006 3 HOH HOH . G 7 HOH A 7 1007 13 HOH HOH . G 7 HOH A 8 1008 1 HOH HOH . G 7 HOH A 9 1009 10 HOH HOH . G 7 HOH A 10 1010 7 HOH HOH . G 7 HOH A 11 1011 9 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 DOC . . . F 6 31.711 10.836 7.903 1 78.72 ? N1 DOC 201 B 1 HETATM 2 C C2 DOC . . . F 6 32.25 9.891 8.867 1 74.17 ? C2 DOC 201 B 1 HETATM 3 N N3 DOC . . . F 6 31.678 9.828 10.15 1 68.25 ? N3 DOC 201 B 1 HETATM 4 C C4 DOC . . . F 6 30.648 10.65 10.439 1 73.06 ? C4 DOC 201 B 1 HETATM 5 C C5 DOC . . . F 6 30.095 11.595 9.498 1 77.37 ? C5 DOC 201 B 1 HETATM 6 C C6 DOC . . . F 6 30.653 11.65 8.253 1 74.34 ? C6 DOC 201 B 1 HETATM 7 O O2 DOC . . . F 6 33.179 9.183 8.531 1 76.56 ? O2 DOC 201 B 1 HETATM 8 N N4 DOC . . . F 6 30.126 10.551 11.704 1 70.01 ? N4 DOC 201 B 1 HETATM 9 C C1' DOC . . . F 6 32.27 10.965 6.524 1 76.73 ? C1' DOC 201 B 1 HETATM 10 C C2' DOC . . . F 6 31.703 9.884 5.578 1 74.39 ? C2' DOC 201 B 1 HETATM 11 C C3' DOC . . . F 6 31.14 10.662 4.394 1 72.98 ? C3' DOC 201 B 1 HETATM 12 C C4' DOC . . . F 6 31.61 12.098 4.601 1 75.9 ? C4' DOC 201 B 1 HETATM 13 O O4' DOC . . . F 6 31.971 12.236 5.974 1 65.01 ? O4' DOC 201 B 1 HETATM 14 C C5' DOC . . . F 6 30.518 13.155 4.328 1 75.91 ? C5' DOC 201 B 1 HETATM 15 O O5' DOC . . . F 6 29.598 13.172 5.381 1 64.49 ? O5' DOC 201 B 1 HETATM 16 P P DOC . . . F 6 28.623 14.453 5.606 1 74.39 ? P DOC 201 B 1 HETATM 17 O OP1 DOC . . . F 6 28.424 15.11 4.165 1 80.17 ? OP1 DOC 201 B 1 HETATM 18 O OP2 DOC . . . F 6 27.328 14.094 6.229 1 81.62 ? OP2 DOC 201 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #