data_7W9S # _model_server_result.job_id qolm-YguoYI-Si7jcBCgXw _model_server_result.datetime_utc '2024-10-19 11:51:06' _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 7w9s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 7W9S # _exptl.entry_id 7W9S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 90 _cell.entry_id 7W9S _cell.length_a 63.992 _cell.length_b 77.663 _cell.length_c 150.831 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W9S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 4 _struct_asym.id D _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 A OD1 ASP 233 A ASP 233 1_555 I MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 A OD2 ASP 233 A ASP 233 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc3 A O TYR 234 A TYR 234 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc4 A NE2 HIS 271 A HIS 271 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc5 A NE2 HIS 273 A HIS 273 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc6 A SG CYS 282 A CYS 282 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc7 A OD1 ASP 329 A ASP 329 1_555 I MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc8 A OD2 ASP 329 A ASP 329 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc9 A OD2 ASP 330 A ASP 330 1_555 I MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc10 A OE2 GLU 343 A GLU 343 1_555 H ZN ZN . A ZN 505 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc11 D O1A CTP . A CTP 501 1_555 I MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc12 D O1A CTP . A CTP 501 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc13 D O2B CTP . A CTP 501 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc14 D O2G CTP . A CTP 501 1_555 J MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc15 I MG MG . A MG 506 1_555 C O3' A 16 C A 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? hydrog WATSON-CRICK hydrog1 B N3 U 21 B U 601 1_555 C N1 A 16 C A 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 U 21 B U 601 1_555 C N6 A 16 C A 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 C 22 B C 602 1_555 C N1 G 15 C G 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 C 22 B C 602 1_555 C O6 G 15 C G 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 C 22 B C 602 1_555 C N2 G 15 C G 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 U 23 B U 603 1_555 C N1 A 14 C A 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 U 23 B U 603 1_555 C N6 A 14 C A 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 C 24 B C 604 1_555 C N1 G 13 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 C 24 B C 604 1_555 C O6 G 13 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 C 24 B C 604 1_555 C N2 G 13 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 U 25 B U 605 1_555 C N1 A 12 C A 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O4 U 25 B U 605 1_555 C N6 A 12 C A 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 C 26 B C 606 1_555 C N1 G 11 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 C 26 B C 606 1_555 C O6 G 11 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 C 26 B C 606 1_555 C N2 G 11 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 U 27 B U 607 1_555 C N1 A 10 C A 695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 U 27 B U 607 1_555 C N6 A 10 C A 695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 C 28 B C 608 1_555 C N1 G 9 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 C 28 B C 608 1_555 C O6 G 9 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 C 28 B C 608 1_555 C N2 G 9 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 G 29 B G 609 1_555 C N3 C 8 C C 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 G 29 B G 609 1_555 C O2 C 8 C C 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 G 29 B G 609 1_555 C N4 C 8 C C 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog24 B N3 U 30 B U 610 1_555 C N1 A 7 C A 692 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 CTP sing 145 n n N1 C6 CTP sing 146 n n N1 C1' CTP sing 147 n n C2 N3 CTP sing 148 n n C2 O2 CTP doub 149 n n N3 C4 CTP doub 150 n n C4 C5 CTP sing 151 n n C4 N4 CTP sing 152 n n C5 C6 CTP doub 153 n n C5 H5 CTP sing 154 n n C6 H6 CTP sing 155 n n N4 HN41 CTP sing 156 n n N4 HN42 CTP sing 157 n n C1' C2' CTP sing 158 n n C1' O4' CTP sing 159 n n C1' H1' CTP sing 160 n n C2' O2' CTP sing 161 n n C2' C3' CTP sing 162 n n C2' H2' CTP sing 163 n n O2' HO2' CTP sing 164 n n C3' C4' CTP sing 165 n n C3' O3' CTP sing 166 n n C3' H3' CTP sing 167 n n C4' O4' CTP sing 168 n n C4' C5' CTP sing 169 n n C4' H4' CTP sing 170 n n O3' HO3' CTP sing 171 n n C5' O5' CTP sing 172 n n C5' "H5'1" CTP sing 173 n n C5' "H5'2" CTP sing 174 n n O5' PA CTP sing 175 n n PA O1A CTP doub 176 n n PA O2A CTP sing 177 n n PA O3A CTP sing 178 n n O2A HOA2 CTP sing 179 n n O3A PB CTP sing 180 n n PB O1B CTP doub 181 n n PB O2B CTP sing 182 n n PB O3B CTP sing 183 n n O2B HOB2 CTP sing 184 n n O3B PG CTP sing 185 n n PG O1G CTP doub 186 n n PG O2G CTP sing 187 n n PG O3G CTP sing 188 n n O2G HOG2 CTP sing 189 n n O3G HOG3 CTP sing 190 n n # _atom_sites.entry_id 7W9S _atom_sites.fract_transf_matrix[1][1] 0.015627 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012876 _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] 0.00663 _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 CTP A 1 501 702 CTP CTP . E 5 SO4 A 1 502 7 SO4 SO4 . F 5 SO4 A 1 503 9 SO4 SO4 . G 5 SO4 A 1 504 10 SO4 SO4 . H 6 ZN A 1 505 2 ZN ZN . I 7 MG A 1 506 1 MG MG . J 7 MG A 1 507 2 MG MG . K 8 HOH A 1 601 3 HOH HOH . K 8 HOH A 2 602 11 HOH HOH . K 8 HOH A 3 603 18 HOH HOH . K 8 HOH A 4 604 24 HOH HOH . K 8 HOH A 5 605 28 HOH HOH . K 8 HOH A 6 606 4 HOH HOH . K 8 HOH A 7 607 27 HOH HOH . K 8 HOH A 8 608 15 HOH HOH . K 8 HOH A 9 609 25 HOH HOH . K 8 HOH A 10 610 16 HOH HOH . K 8 HOH A 11 611 20 HOH HOH . K 8 HOH A 12 612 14 HOH HOH . K 8 HOH A 13 613 13 HOH HOH . K 8 HOH A 14 614 21 HOH HOH . K 8 HOH A 15 615 26 HOH HOH . L 8 HOH B 1 701 12 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 CTP . . . D 4 -12.689 -8.884 14.987 1 64.85 ? N1 CTP 501 A 1 HETATM 2 C C2 CTP . . . D 4 -13.651 -7.961 15.374 1 65.94 ? C2 CTP 501 A 1 HETATM 3 N N3 CTP . . . D 4 -13.26 -6.724 15.883 1 63.19 ? N3 CTP 501 A 1 HETATM 4 C C4 CTP . . . D 4 -11.922 -6.387 15.941 1 57.88 ? C4 CTP 501 A 1 HETATM 5 C C5 CTP . . . D 4 -10.975 -7.301 15.5 1 58.04 ? C5 CTP 501 A 1 HETATM 6 C C6 CTP . . . D 4 -11.359 -8.59 15.163 1 61.2 ? C6 CTP 501 A 1 HETATM 7 O O2 CTP . . . D 4 -14.845 -8.255 15.23 1 62.27 ? O2 CTP 501 A 1 HETATM 8 N N4 CTP . . . D 4 -11.545 -5.209 16.425 1 56.18 ? N4 CTP 501 A 1 HETATM 9 C C1' CTP . . . D 4 -13.109 -10.16 14.374 1 62.52 ? C1' CTP 501 A 1 HETATM 10 C C2' CTP . . . D 4 -13.338 -9.986 12.88 1 59.89 ? C2' CTP 501 A 1 HETATM 11 O O2' CTP . . . D 4 -14.417 -10.793 12.457 1 58.12 ? O2' CTP 501 A 1 HETATM 12 C C3' CTP . . . D 4 -12.067 -10.505 12.244 1 62.28 ? C3' CTP 501 A 1 HETATM 13 C C4' CTP . . . D 4 -11.645 -11.578 13.235 1 64.79 ? C4' CTP 501 A 1 HETATM 14 O O4' CTP . . . D 4 -12.064 -11.111 14.513 1 63.9 ? O4' CTP 501 A 1 HETATM 15 O O3' CTP . . . D 4 -12.24 -11.009 10.933 1 58.81 ? O3' CTP 501 A 1 HETATM 16 C C5' CTP . . . D 4 -10.151 -11.882 13.158 1 64.32 ? C5' CTP 501 A 1 HETATM 17 O O5' CTP . . . D 4 -9.382 -10.964 13.902 1 63.17 ? O5' CTP 501 A 1 HETATM 18 P PA CTP . . . D 4 -8.014 -10.421 13.284 1 70.4 ? PA CTP 501 A 1 HETATM 19 O O1A CTP . . . D 4 -7.07 -11.571 13.046 1 68.03 -1 O1A CTP 501 A 1 HETATM 20 O O2A CTP . . . D 4 -7.415 -9.425 14.258 1 75.94 ? O2A CTP 501 A 1 HETATM 21 O O3A CTP . . . D 4 -8.363 -9.658 11.876 1 70.49 ? O3A CTP 501 A 1 HETATM 22 P PB CTP . . . D 4 -8.422 -10.304 10.38 1 64.26 ? PB CTP 501 A 1 HETATM 23 O O1B CTP . . . D 4 -9.803 -10.116 9.822 1 58.29 -1 O1B CTP 501 A 1 HETATM 24 O O2B CTP . . . D 4 -8.101 -11.786 10.369 1 63.2 ? O2B CTP 501 A 1 HETATM 25 O O3B CTP . . . D 4 -7.337 -9.485 9.527 1 64.58 ? O3B CTP 501 A 1 HETATM 26 P PG CTP . . . D 4 -5.769 -9.819 9.543 1 79.78 ? PG CTP 501 A 1 HETATM 27 O O1G CTP . . . D 4 -5.356 -10.266 8.159 1 76.26 -1 O1G CTP 501 A 1 HETATM 28 O O2G CTP . . . D 4 -5.448 -10.846 10.613 1 65.83 ? O2G CTP 501 A 1 HETATM 29 O O3G CTP . . . D 4 -5.006 -8.534 9.87 1 83.03 -1 O3G CTP 501 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #