data_5CR0 # _model_server_result.job_id T5k3xmKy7fRGKvQqyXgwDg _model_server_result.datetime_utc '2024-11-24 11:39:34' _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 5cr0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 5CR0 # _exptl.entry_id 5CR0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _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 5CR0 _cell.length_a 84.511 _cell.length_b 84.511 _cell.length_c 399.101 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CR0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # 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 trimeric 3 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,I,J 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 # _struct_asym.details ? _struct_asym.entity_id 5 _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 302 A CYS 543 1_555 B SG CYS 302 B CYS 543 6_664 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 B OD1 ASP 186 B ASP 427 1_555 E MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 B OD1 ASP 188 B ASP 429 1_555 E MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc3 E MG MG . B MG 601 1_555 F O2A DCP . B DCP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc4 E MG MG . B MG 601 1_555 F O2B DCP . B DCP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc5 E MG MG . B MG 601 1_555 F O2G DCP . B DCP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? hydrog WATSON-CRICK hydrog1 C N3 DC 1 P DC 1 1_555 D N1 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N4 DC 1 P DC 1 1_555 D O6 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O2 DC 1 P DC 1 1_555 D N2 DG 6 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N1 DA 2 P DA 2 1_555 D N3 DT 5 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N6 DA 2 P DA 2 1_555 D O4 DT 5 T DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N1 DG 3 P DG 3 1_555 D N3 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N2 DG 3 P DG 3 1_555 D O2 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O6 DG 3 P DG 3 1_555 D N4 DC 4 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N3 DT 4 P DT 4 1_555 D N1 DA 3 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C O4 DT 4 P DT 4 1_555 D N6 DA 3 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N1 DA 5 P DA 5 1_555 D N3 DT 2 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N6 DA 5 P DA 5 1_555 D O4 DT 2 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DC 6 P DC 6 1_555 D N1 DG 1 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N4 DC 6 P DC 6 1_555 D O6 DG 1 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O2 DC 6 P DC 6 1_555 D N2 DG 1 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DCP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _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 N1 C2 DCP sing 156 n n N1 C6 DCP sing 157 n n N1 C1' DCP sing 158 n n C2 N3 DCP sing 159 n n C2 O2 DCP doub 160 n n N3 C4 DCP doub 161 n n C4 C5 DCP sing 162 n n C4 N4 DCP sing 163 n n C5 C6 DCP doub 164 n n C5 H5 DCP sing 165 n n C6 H6 DCP sing 166 n n N4 HN41 DCP sing 167 n n N4 HN42 DCP sing 168 n n C1' C2' DCP sing 169 n n C1' O4' DCP sing 170 n n C1' H1' DCP sing 171 n n C2' C3' DCP sing 172 n n C2' "H2'1" DCP sing 173 n n C2' "H2'2" DCP sing 174 n n C3' C4' DCP sing 175 n n C3' O3' DCP sing 176 n n C3' H3' DCP sing 177 n n C4' O4' DCP sing 178 n n C4' C5' DCP sing 179 n n C4' H4' DCP sing 180 n n O3' HO3' DCP sing 181 n n C5' O5' DCP sing 182 n n C5' "H5'1" DCP sing 183 n n C5' "H5'2" DCP sing 184 n n O5' PA DCP sing 185 n n PA O1A DCP doub 186 n n PA O2A DCP sing 187 n n PA O3A DCP sing 188 n n O2A HOA2 DCP sing 189 n n O3A PB DCP sing 190 n n PB O1B DCP doub 191 n n PB O2B DCP sing 192 n n PB O3B DCP sing 193 n n O2B HOB2 DCP sing 194 n n O3B PG DCP sing 195 n n PG O1G DCP doub 196 n n PG O2G DCP sing 197 n n PG O3G DCP sing 198 n n O2G HOG2 DCP sing 199 n n O3G HOG3 DCP sing 200 n n # _atom_sites.entry_id 5CR0 _atom_sites.fract_transf_matrix[1][1] 0.011833 _atom_sites.fract_transf_matrix[1][2] 0.006832 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013663 _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] 0.002506 _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 E 4 MG B 1 601 601 MG MG . F 5 DCP B 1 602 602 DCP DCP . G 6 HOH A 1 601 9 HOH HOH . G 6 HOH A 2 602 1 HOH HOH . G 6 HOH A 3 603 2 HOH HOH . H 6 HOH B 1 701 3 HOH HOH . H 6 HOH B 2 702 6 HOH HOH . H 6 HOH B 3 703 5 HOH HOH . H 6 HOH B 4 704 4 HOH HOH . H 6 HOH B 5 705 7 HOH HOH . I 6 HOH P 1 101 8 HOH HOH . J 6 HOH T 1 101 10 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 DCP . . . F 5 -24.775 35.742 53.021 1 68.06 ? N1 DCP 602 B 1 HETATM 2 C C2 DCP . . . F 5 -24.674 34.972 54.207 1 66.37 ? C2 DCP 602 B 1 HETATM 3 N N3 DCP . . . F 5 -23.49 34.161 54.385 1 63.57 ? N3 DCP 602 B 1 HETATM 4 C C4 DCP . . . F 5 -22.542 34.16 53.46 1 64.95 ? C4 DCP 602 B 1 HETATM 5 C C5 DCP . . . F 5 -22.683 35.004 52.205 1 69.13 ? C5 DCP 602 B 1 HETATM 6 C C6 DCP . . . F 5 -23.787 35.767 52.026 1 63.61 ? C6 DCP 602 B 1 HETATM 7 O O2 DCP . . . F 5 -25.549 34.974 55.06 1 61.53 ? O2 DCP 602 B 1 HETATM 8 N N4 DCP . . . F 5 -21.372 33.356 53.639 1 70.62 ? N4 DCP 602 B 1 HETATM 9 C C1' DCP . . . F 5 -25.954 36.589 52.799 1 62.93 ? C1' DCP 602 B 1 HETATM 10 C C2' DCP . . . F 5 -25.831 37.885 53.538 1 63.79 ? C2' DCP 602 B 1 HETATM 11 C C3' DCP . . . F 5 -25.518 38.855 52.457 1 63.73 ? C3' DCP 602 B 1 HETATM 12 C C4' DCP . . . F 5 -26.26 38.274 51.309 1 64.88 ? C4' DCP 602 B 1 HETATM 13 O O4' DCP . . . F 5 -26.157 36.891 51.436 1 68.38 ? O4' DCP 602 B 1 HETATM 14 O O3' DCP . . . F 5 -25.929 40.149 52.761 1 59.94 ? O3' DCP 602 B 1 HETATM 15 C C5' DCP . . . F 5 -25.684 38.747 49.98 1 58.53 ? C5' DCP 602 B 1 HETATM 16 O O5' DCP . . . F 5 -24.392 38.232 49.9 1 60.78 ? O5' DCP 602 B 1 HETATM 17 P PA DCP . . . F 5 -23.162 39.05 49.31 1 59.9 ? PA DCP 602 B 1 HETATM 18 O O1A DCP . . . F 5 -22.037 38.059 49.11 1 47.88 ? O1A DCP 602 B 1 HETATM 19 O O2A DCP . . . F 5 -23.543 39.66 47.982 1 56.4 ? O2A DCP 602 B 1 HETATM 20 O O3A DCP . . . F 5 -22.629 40.153 50.305 1 53.58 ? O3A DCP 602 B 1 HETATM 21 P PB DCP . . . F 5 -23.19 41.625 50.443 1 53.16 ? PB DCP 602 B 1 HETATM 22 O O1B DCP . . . F 5 -23.701 41.833 51.845 1 62.51 ? O1B DCP 602 B 1 HETATM 23 O O2B DCP . . . F 5 -24.325 41.901 49.481 1 58.81 ? O2B DCP 602 B 1 HETATM 24 O O3B DCP . . . F 5 -21.993 42.617 50.199 1 61.4 ? O3B DCP 602 B 1 HETATM 25 P PG DCP . . . F 5 -21.4 42.917 48.765 1 57.96 ? PG DCP 602 B 1 HETATM 26 O O1G DCP . . . F 5 -19.932 42.56 48.725 1 50.8 ? O1G DCP 602 B 1 HETATM 27 O O2G DCP . . . F 5 -22.133 42.131 47.7 1 48.72 ? O2G DCP 602 B 1 HETATM 28 O O3G DCP . . . F 5 -21.528 44.397 48.489 1 50.64 ? O3G DCP 602 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #