data_6QCV # _model_server_result.job_id Po13N7_qkdo-s83BxnrlxQ _model_server_result.datetime_utc '2024-10-10 10:24:29' _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 6qcv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":801}' # _entry.id 6QCV # _exptl.entry_id 6QCV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 8 _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 120 _cell.entry_id 6QCV _cell.length_a 200.191 _cell.length_b 200.191 _cell.length_c 256.208 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QCV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 8 _struct_asym.id H _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 D O3B M7G 1 M M7G 0 1_555 D P G 2 M G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 B OD2 ASP 314 B ASP 305 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc2 B O ASN 315 B ASN 306 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc3 B OD2 ASP 453 B ASP 444 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc4 H O2B CTP . B CTP 801 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc5 H O2G CTP . B CTP 801 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? hydrog 'A-U PAIR' hydrog1 D N7 A 9 M A 8 1_555 E N3 U 21 R U 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N1 A 12 M A 11 1_555 E N3 U 20 R U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N6 A 12 M A 11 1_555 E O4 U 20 R U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N3 U 13 M U 12 1_555 E N1 A 19 R A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D O4 U 13 M U 12 1_555 E N6 A 19 R A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N1 A 14 M A 13 1_555 E N3 U 18 R U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N6 A 14 M A 13 1_555 E O4 U 18 R U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N1 G 15 M G 14 1_555 E N3 C 17 R C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N2 G 15 M G 14 1_555 E O2 C 17 R C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O6 G 15 M G 14 1_555 E N4 C 17 R C 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N3 C 6 R C 6 1_555 F N1 G 14 V G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E N4 C 6 R C 6 1_555 F O6 G 14 V G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E O2 C 6 R C 6 1_555 F N2 G 14 V G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N3 U 7 R U 7 1_555 F N1 A 13 V A 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E O4 U 7 R U 7 1_555 F N6 A 13 V A 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E N3 C 8 R C 8 1_555 F N1 G 12 V G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N4 C 8 R C 8 1_555 F O6 G 12 V G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E O2 C 8 R C 8 1_555 F N2 G 12 V G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E N3 U 9 R U 9 1_555 F N1 A 11 V A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E O4 U 9 R U 9 1_555 F N6 A 11 V A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog21 F N6 A 1 V A 1 1_555 F N3 A 10 V A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 F N1 G 2 V G 2 1_555 F N3 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 F N2 G 2 V G 2 1_555 F O2 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 F O6 G 2 V G 2 1_555 F N4 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 F N3 U 3 V U 3 1_555 F N1 A 8 V A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 F O4 U 3 V U 3 1_555 F N6 A 8 V A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog27 F N3 A 4 V A 4 1_555 F N6 A 7 V A 7 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 6QCV _atom_sites.fract_transf_matrix[1][1] 0.004995 _atom_sites.fract_transf_matrix[1][2] 0.002884 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005768 _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] 0.003903 _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 G 7 PO4 A 1 801 2 PO4 PO4 . H 8 CTP B 1 801 1 CTP CTP . I 9 MG B 1 802 1 MG MG . # 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 . . . H 8 -55.186 35.952 -17.58 1 128.22 ? N1 CTP 801 B 1 HETATM 2 C C2 CTP . . . H 8 -55.125 36.675 -18.775 1 127.3 ? C2 CTP 801 B 1 HETATM 3 N N3 CTP . . . H 8 -55.292 38.02 -18.745 1 124.91 ? N3 CTP 801 B 1 HETATM 4 C C4 CTP . . . H 8 -55.52 38.651 -17.586 1 123.3 ? C4 CTP 801 B 1 HETATM 5 C C5 CTP . . . H 8 -55.596 37.932 -16.362 1 124.16 ? C5 CTP 801 B 1 HETATM 6 C C6 CTP . . . H 8 -55.425 36.601 -16.403 1 126.41 ? C6 CTP 801 B 1 HETATM 7 O O2 CTP . . . H 8 -54.908 36.062 -19.831 1 129.43 ? O2 CTP 801 B 1 HETATM 8 N N4 CTP . . . H 8 -55.681 39.966 -17.613 1 121.62 ? N4 CTP 801 B 1 HETATM 9 C C1' CTP . . . H 8 -55 34.474 -17.644 1 132.37 ? C1' CTP 801 B 1 HETATM 10 C C2' CTP . . . H 8 -53.554 34.057 -17.93 1 135.75 ? C2' CTP 801 B 1 HETATM 11 O O2' CTP . . . H 8 -53.557 32.801 -18.577 1 139.73 ? O2' CTP 801 B 1 HETATM 12 C C3' CTP . . . H 8 -52.999 33.989 -16.506 1 136.5 ? C3' CTP 801 B 1 HETATM 13 C C4' CTP . . . H 8 -54.17 33.314 -15.782 1 136.71 ? C4' CTP 801 B 1 HETATM 14 O O4' CTP . . . H 8 -55.345 33.904 -16.399 1 133.57 ? O4' CTP 801 B 1 HETATM 15 O O3' CTP . . . H 8 -51.815 33.208 -16.412 1 140.64 ? O3' CTP 801 B 1 HETATM 16 C C5' CTP . . . H 8 -54.231 33.481 -14.282 1 136.89 ? C5' CTP 801 B 1 HETATM 17 O O5' CTP . . . H 8 -53.972 34.862 -13.916 1 133.94 ? O5' CTP 801 B 1 HETATM 18 P PA CTP . . . H 8 -53.721 35.211 -12.368 1 134.83 ? PA CTP 801 B 1 HETATM 19 O O1A CTP . . . H 8 -54.131 36.623 -12.104 1 131.32 ? O1A CTP 801 B 1 HETATM 20 O O2A CTP . . . H 8 -54.323 34.145 -11.512 1 138 ? O2A CTP 801 B 1 HETATM 21 O O3A CTP . . . H 8 -52.119 35.111 -12.28 1 137.69 ? O3A CTP 801 B 1 HETATM 22 P PB CTP . . . H 8 -51.047 33.922 -12.393 1 142.76 ? PB CTP 801 B 1 HETATM 23 O O1B CTP . . . H 8 -50.804 33.611 -13.833 1 142.71 ? O1B CTP 801 B 1 HETATM 24 O O2B CTP . . . H 8 -51.449 32.824 -11.469 1 146.93 ? O2B CTP 801 B 1 HETATM 25 O O3B CTP . . . H 8 -49.744 34.631 -11.79 1 143.8 ? O3B CTP 801 B 1 HETATM 26 P PG CTP . . . H 8 -49.143 34.742 -10.295 1 146.88 ? PG CTP 801 B 1 HETATM 27 O O1G CTP . . . H 8 -48.072 33.685 -10.203 1 152.58 ? O1G CTP 801 B 1 HETATM 28 O O2G CTP . . . H 8 -50.298 34.482 -9.361 1 147.24 ? O2G CTP 801 B 1 HETATM 29 O O3G CTP . . . H 8 -48.591 36.143 -10.165 1 144.04 ? O3G CTP 801 B 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #