data_3JB7 # _model_server_result.job_id '_hgFr1HjJgixCn9xRkoMnQ' _model_server_result.datetime_utc '2024-11-22 09:00:37' _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 3jb7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1302}' # _entry.id 3JB7 # _exptl.entry_id 3JB7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 483.156 _entity.id 7 _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 3JB7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JB7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 7 _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 hydrog WATSON-CRICK hydrog1 D N1 G 2 t G 1 1_555 E N3 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N2 G 2 t G 1 1_555 E O2 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D O6 G 2 t G 1 1_555 E N4 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog4 D N1 G 3 t G 2 1_555 E O2 C 4 m C 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N1 G 3 t G 2 1_555 E N3 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N2 G 3 t G 2 1_555 E O2 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D O6 G 3 t G 2 1_555 E N4 C 5 m C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N1 G 4 t G 3 1_555 E N3 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N2 G 4 t G 3 1_555 E O2 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O6 G 4 t G 3 1_555 E N4 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N1 G 5 t G 4 1_555 E N3 C 2 m C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N2 G 5 t G 4 1_555 E O2 C 2 m C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D O6 G 5 t G 4 1_555 E N4 C 2 m C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N1 G 5 t G 4 1_555 E N3 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N2 G 5 t G 4 1_555 E O2 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D O6 G 5 t G 4 1_555 E N4 C 3 m C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog17 D N1 G 6 t G 5 1_555 E N3 C 1 m C 1 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 106 n n N1 C6 CTP sing 107 n n N1 C1' CTP sing 108 n n C2 N3 CTP sing 109 n n C2 O2 CTP doub 110 n n N3 C4 CTP doub 111 n n C4 C5 CTP sing 112 n n C4 N4 CTP sing 113 n n C5 C6 CTP doub 114 n n C5 H5 CTP sing 115 n n C6 H6 CTP sing 116 n n N4 HN41 CTP sing 117 n n N4 HN42 CTP sing 118 n n C1' C2' CTP sing 119 n n C1' O4' CTP sing 120 n n C1' H1' CTP sing 121 n n C2' O2' CTP sing 122 n n C2' C3' CTP sing 123 n n C2' H2' CTP sing 124 n n O2' HO2' CTP sing 125 n n C3' C4' CTP sing 126 n n C3' O3' CTP sing 127 n n C3' H3' CTP sing 128 n n C4' O4' CTP sing 129 n n C4' C5' CTP sing 130 n n C4' H4' CTP sing 131 n n O3' HO3' CTP sing 132 n n C5' O5' CTP sing 133 n n C5' "H5'1" CTP sing 134 n n C5' "H5'2" CTP sing 135 n n O5' PA CTP sing 136 n n PA O1A CTP doub 137 n n PA O2A CTP sing 138 n n PA O3A CTP sing 139 n n O2A HOA2 CTP sing 140 n n O3A PB CTP sing 141 n n PB O1B CTP doub 142 n n PB O2B CTP sing 143 n n PB O3B CTP sing 144 n n O2B HOB2 CTP sing 145 n n O3B PG CTP sing 146 n n PG O1G CTP doub 147 n n PG O2G CTP sing 148 n n PG O3G CTP sing 149 n n O2G HOG2 CTP sing 150 n n O3G HOG3 CTP sing 151 n n # _atom_sites.entry_id 3JB7 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 6 GTP A 1 1301 1301 GTP GTP . H 7 CTP A 1 1302 1302 CTP CTP . I 6 GTP B 1 601 601 GTP GTP . # 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 7 115.91 -33.046 177.72 1 200.99 ? N1 CTP 1302 A 1 HETATM 2 C C2 CTP . . . H 7 115.741 -32.059 178.671 1 200.25 ? C2 CTP 1302 A 1 HETATM 3 N N3 CTP . . . H 7 115.3 -30.813 178.279 1 195.84 ? N3 CTP 1302 A 1 HETATM 4 C C4 CTP . . . H 7 114.574 -30.718 177.112 1 197.9 ? C4 CTP 1302 A 1 HETATM 5 C C5 CTP . . . H 7 114.729 -31.707 176.151 1 200.47 ? C5 CTP 1302 A 1 HETATM 6 C C6 CTP . . . H 7 115.2 -32.951 176.558 1 201.43 ? C6 CTP 1302 A 1 HETATM 7 O O2 CTP . . . H 7 115.981 -32.285 179.856 1 203.46 ? O2 CTP 1302 A 1 HETATM 8 N N4 CTP . . . H 7 113.733 -29.707 176.916 1 200.24 ? N4 CTP 1302 A 1 HETATM 9 C C1' CTP . . . H 7 117.161 -33.828 177.733 1 199.1 ? C1' CTP 1302 A 1 HETATM 10 C C2' CTP . . . H 7 116.888 -35.308 177.937 1 195.18 ? C2' CTP 1302 A 1 HETATM 11 O O2' CTP . . . H 7 117.071 -35.654 179.288 1 191.59 ? O2' CTP 1302 A 1 HETATM 12 C C3' CTP . . . H 7 117.933 -36.004 177.09 1 202.73 ? C3' CTP 1302 A 1 HETATM 13 C C4' CTP . . . H 7 118.623 -34.896 176.307 1 211.3 ? C4' CTP 1302 A 1 HETATM 14 O O4' CTP . . . H 7 117.853 -33.724 176.503 1 203.49 ? O4' CTP 1302 A 1 HETATM 15 O O3' CTP . . . H 7 118.857 -36.658 177.925 1 205.01 ? O3' CTP 1302 A 1 HETATM 16 C C5' CTP . . . H 7 118.774 -35.242 174.827 1 230.25 ? C5' CTP 1302 A 1 HETATM 17 O O5' CTP . . . H 7 119.688 -34.351 174.222 1 246.75 ? O5' CTP 1302 A 1 HETATM 18 P PA CTP . . . H 7 119.688 -34.103 172.629 1 259.02 ? PA CTP 1302 A 1 HETATM 19 O O1A CTP . . . H 7 118.311 -34.368 172.068 1 264.43 ? O1A CTP 1302 A 1 HETATM 20 O O2A CTP . . . H 7 120.143 -32.701 172.3 1 262.52 ? O2A CTP 1302 A 1 HETATM 21 O O3A CTP . . . H 7 120.713 -35.191 172.034 1 258.08 ? O3A CTP 1302 A 1 HETATM 22 P PB CTP . . . H 7 122.209 -34.726 171.662 1 255.56 ? PB CTP 1302 A 1 HETATM 23 O O1B CTP . . . H 7 122.162 -33.819 170.455 1 254.54 ? O1B CTP 1302 A 1 HETATM 24 O O2B CTP . . . H 7 123.095 -35.92 171.403 1 259.48 ? O2B CTP 1302 A 1 HETATM 25 O O3B CTP . . . H 7 122.671 -33.898 172.968 1 260.16 ? O3B CTP 1302 A 1 HETATM 26 P PG CTP . . . H 7 124.19 -33.403 173.185 1 255.65 ? PG CTP 1302 A 1 HETATM 27 O O1G CTP . . . H 7 125.011 -34.553 173.717 1 254.28 ? O1G CTP 1302 A 1 HETATM 28 O O2G CTP . . . H 7 124.226 -32.268 174.182 1 250.86 ? O2G CTP 1302 A 1 HETATM 29 O O3G CTP . . . H 7 124.754 -32.935 171.866 1 259.96 ? O3G CTP 1302 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 427 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 29 #