data_2BPF # _model_server_result.job_id VrliRlMcB6og5GHgYlvZ2g _model_server_result.datetime_utc '2024-11-24 20:25:31' _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 2bpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":338}' # _entry.id 2BPF # _exptl.entry_id 2BPF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 451.158 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXYCYTIDINE 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 2BPF _cell.length_a 94.9 _cell.length_b 94.9 _cell.length_c 117.6 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _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,H,I _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 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 metalc ? metalc1 C O ASP 190 A ASP 190 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc2 C OD1 ASP 190 A ASP 190 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc3 C OD2 ASP 190 A ASP 190 1_555 E MG MG . A MG 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc4 C OD2 ASP 192 A ASP 192 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc5 C OD1 ASP 192 A ASP 192 1_555 E MG MG . A MG 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc6 F O2B DCT . A DCT 338 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? metalc ? metalc7 F O1A DCT . A DCT 338 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc8 F O1G DCT . A DCT 338 1_555 D MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc9 F O1A DCT . A DCT 338 1_555 E MG MG . A MG 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc10 D MG MG . A MG 339 1_555 I O HOH . A HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? hydrog WATSON-CRICK hydrog1 A N1 DG 2 T DG 5 1_555 B N3 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 2 T DG 5 1_555 B O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 2 T DG 5 1_555 B N4 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 3 T DG 6 1_555 B N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 3 T DG 6 1_555 B O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 3 T DG 6 1_555 B N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 4 T DC 7 1_555 B N1 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 4 T DC 7 1_555 B O6 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 4 T DC 7 1_555 B N2 DG 5 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 5 T DG 8 1_555 B N3 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 5 T DG 8 1_555 B O2 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 5 T DG 8 1_555 B N4 DC 4 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 6 T DC 9 1_555 B N1 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 6 T DC 9 1_555 B O6 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 6 T DC 9 1_555 B N2 DG 3 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 7 T DC 10 1_555 B N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 7 T DC 10 1_555 B O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 7 T DC 10 1_555 B N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DG 8 T DG 11 1_555 B N3 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 DG 8 T DG 11 1_555 B O2 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 DG 8 T DG 11 1_555 B N4 DC 1 P DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O12 P3' _chem_comp.formula_weight 451.158 _chem_comp.id DCT _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE" _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 DCT sing 118 n n N1 C6 DCT sing 119 n n N1 C1' DCT sing 120 n n C2 N3 DCT sing 121 n n C2 O2 DCT doub 122 n n N3 C4 DCT doub 123 n n C4 C5 DCT sing 124 n n C4 N4 DCT sing 125 n n C5 C6 DCT doub 126 n n C5 H5 DCT sing 127 n n C6 H6 DCT sing 128 n n N4 HN41 DCT sing 129 n n N4 HN42 DCT sing 130 n n C1' C2' DCT sing 131 n n C1' O4' DCT sing 132 n n C1' H1' DCT sing 133 n n C2' C3' DCT sing 134 n n C2' H2' DCT sing 135 n n C2' "H2''" DCT sing 136 n n C3' C4' DCT sing 137 n n C3' "H3'1" DCT sing 138 n n C3' "H3'2" DCT sing 139 n n C4' O4' DCT sing 140 n n C4' C5' DCT sing 141 n n C4' H4' DCT sing 142 n n C5' O5' DCT sing 143 n n C5' H5' DCT sing 144 n n C5' "H5''" DCT sing 145 n n O5' PA DCT sing 146 n n PA O1A DCT doub 147 n n PA O2A DCT sing 148 n n PA O3A DCT sing 149 n n O2A HOA2 DCT sing 150 n n O3A PB DCT sing 151 n n PB O1B DCT doub 152 n n PB O2B DCT sing 153 n n PB O3B DCT sing 154 n n O2B HOB2 DCT sing 155 n n O3B PG DCT sing 156 n n PG O1G DCT doub 157 n n PG O2G DCT sing 158 n n PG O3G DCT sing 159 n n O2G HOG2 DCT sing 160 n n O3G HOG3 DCT sing 161 n n # _atom_sites.entry_id 2BPF _atom_sites.fract_transf_matrix[1][1] 0.010537 _atom_sites.fract_transf_matrix[1][2] 0.006084 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012168 _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] 0.008503 _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 MG A 1 339 339 MG MG . E 4 MG A 1 340 340 MG MG . F 5 DCT A 1 338 338 DCT DCT . G 6 HOH T 1 410 410 HOH HOH . G 6 HOH T 2 417 417 HOH HOH . H 6 HOH P 1 401 401 HOH HOH . H 6 HOH P 2 411 411 HOH HOH . I 6 HOH A 1 400 400 HOH HOH . I 6 HOH A 2 402 402 HOH HOH . I 6 HOH A 3 403 403 HOH HOH . I 6 HOH A 4 404 404 HOH HOH . I 6 HOH A 5 405 405 HOH HOH . I 6 HOH A 6 406 406 HOH HOH . I 6 HOH A 7 407 407 HOH HOH . I 6 HOH A 8 408 408 HOH HOH . I 6 HOH A 9 409 409 HOH HOH . I 6 HOH A 10 412 412 HOH HOH . I 6 HOH A 11 413 413 HOH HOH . I 6 HOH A 12 414 414 HOH HOH . I 6 HOH A 13 415 415 HOH HOH . I 6 HOH A 14 416 416 HOH HOH . I 6 HOH A 15 418 418 HOH HOH . I 6 HOH A 16 419 419 HOH HOH . I 6 HOH A 17 420 420 HOH HOH . I 6 HOH A 18 421 421 HOH HOH . I 6 HOH A 19 422 422 HOH HOH . I 6 HOH A 20 423 423 HOH HOH . I 6 HOH A 21 424 424 HOH HOH . I 6 HOH A 22 425 425 HOH HOH . I 6 HOH A 23 426 426 HOH HOH . I 6 HOH A 24 427 427 HOH HOH . I 6 HOH A 25 428 428 HOH HOH . I 6 HOH A 26 429 429 HOH HOH . I 6 HOH A 27 430 430 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 DCT . . . F 5 7.981 65.909 19.596 1 12.76 ? N1 DCT 338 A 1 HETATM 2 C C2 DCT . . . F 5 6.672 65.691 20.113 1 19.61 ? C2 DCT 338 A 1 HETATM 3 N N3 DCT . . . F 5 6.228 64.397 20.177 1 13.84 ? N3 DCT 338 A 1 HETATM 4 C C4 DCT . . . F 5 7.01 63.394 19.752 1 4.02 ? C4 DCT 338 A 1 HETATM 5 C C5 DCT . . . F 5 8.282 63.624 19.222 1 1 ? C5 DCT 338 A 1 HETATM 6 C C6 DCT . . . F 5 8.725 64.862 19.164 1 1.04 ? C6 DCT 338 A 1 HETATM 7 O O2 DCT . . . F 5 5.963 66.65 20.518 1 21.98 ? O2 DCT 338 A 1 HETATM 8 N N4 DCT . . . F 5 6.527 62.151 19.82 1 3.36 ? N4 DCT 338 A 1 HETATM 9 C C1' DCT . . . F 5 9.206 66.742 19.326 1 13.61 ? C1' DCT 338 A 1 HETATM 10 C C2' DCT . . . F 5 10.338 66.714 20.353 1 1 ? C2' DCT 338 A 1 HETATM 11 C C3' DCT . . . F 5 11.447 67.276 19.457 1 5.39 ? C3' DCT 338 A 1 HETATM 12 C C4' DCT . . . F 5 11.219 66.506 18.158 1 11.78 ? C4' DCT 338 A 1 HETATM 13 O O4' DCT . . . F 5 9.772 66.437 18.036 1 17.82 ? O4' DCT 338 A 1 HETATM 14 C C5' DCT . . . F 5 11.65 65.071 18.243 1 14.86 ? C5' DCT 338 A 1 HETATM 15 O O5' DCT . . . F 5 12.915 64.969 17.801 1 19.89 ? O5' DCT 338 A 1 HETATM 16 P PA DCT . . . F 5 13.617 63.613 18.171 1 18.62 ? PA DCT 338 A 1 HETATM 17 O O1A DCT . . . F 5 14.847 63.666 17.242 1 1 ? O1A DCT 338 A 1 HETATM 18 O O2A DCT . . . F 5 12.518 62.466 18.2 1 19.21 ? O2A DCT 338 A 1 HETATM 19 O O3A DCT . . . F 5 14.052 63.897 19.666 1 20.21 ? O3A DCT 338 A 1 HETATM 20 P PB DCT . . . F 5 15.315 64.577 20.055 1 16.96 ? PB DCT 338 A 1 HETATM 21 O O1B DCT . . . F 5 15.121 65.508 21.165 1 6.45 ? O1B DCT 338 A 1 HETATM 22 O O2B DCT . . . F 5 15.932 65.097 18.678 1 10.01 ? O2B DCT 338 A 1 HETATM 23 O O3B DCT . . . F 5 16.053 63.336 20.467 1 20.1 ? O3B DCT 338 A 1 HETATM 24 P PG DCT . . . F 5 17.289 62.589 19.674 1 22.72 ? PG DCT 338 A 1 HETATM 25 O O1G DCT . . . F 5 17.329 63.113 18.206 1 21.66 ? O1G DCT 338 A 1 HETATM 26 O O2G DCT . . . F 5 18.45 62.804 20.495 1 17.57 ? O2G DCT 338 A 1 HETATM 27 O O3G DCT . . . F 5 16.878 61.167 19.7 1 27.66 ? O3G DCT 338 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #