data_8K8U # _model_server_result.job_id XujFdJnaBn43dwETHC2XAg _model_server_result.datetime_utc '2025-07-19 17:28:04' _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 8k8u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1104}' # _entry.id 8K8U # _exptl.entry_id 8K8U _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 8K8U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8K8U _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 I _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 549 A ASP 549 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc2 A OD2 ASP 549 A ASP 549 1_555 G MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc3 A O TYR 550 A TYR 550 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc4 A OD2 ASP 753 A ASP 753 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc5 F MG MG . A MG 1101 1_555 I O1B CTP . A CTP 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 F MG MG . A MG 1101 1_555 I O3G CTP . A CTP 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc7 H MG MG . A MG 1103 1_555 I O1G CTP . A CTP 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? hydrog WATSON-CRICK hydrog1 D N1 DA 1 E DA 14 1_555 E N3 DT 16 F DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N6 DA 1 E DA 14 1_555 E O4 DT 16 F DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N3 DT 2 E DT 15 1_555 E N1 DA 15 F DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D O4 DT 2 E DT 15 1_555 E N6 DA 15 F DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N3 DC 3 E DC 16 1_555 E N1 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N4 DC 3 E DC 16 1_555 E O6 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D O2 DC 3 E DC 16 1_555 E N2 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N3 DC 4 E DC 17 1_555 E N1 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N4 DC 4 E DC 17 1_555 E O6 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O2 DC 4 E DC 17 1_555 E N2 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N3 DT 5 E DT 18 1_555 E N1 DA 12 F DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D O4 DT 5 E DT 18 1_555 E N6 DA 12 F DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N3 DC 6 E DC 19 1_555 E N1 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N4 DC 6 E DC 19 1_555 E O6 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D O2 DC 6 E DC 19 1_555 E N2 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D N3 DC 7 E DC 20 1_555 E N1 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N4 DC 7 E DC 20 1_555 E O6 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D O2 DC 7 E DC 20 1_555 E N2 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D N3 DC 8 E DC 21 1_555 E N1 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N4 DC 8 E DC 21 1_555 E O6 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D O2 DC 8 E DC 21 1_555 E N2 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N3 DC 9 E DC 22 1_555 E N1 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N4 DC 9 E DC 22 1_555 E O6 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D O2 DC 9 E DC 22 1_555 E N2 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N3 DT 10 E DT 23 1_555 E N1 DA 7 F DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D O4 DT 10 E DT 23 1_555 E N6 DA 7 F DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N1 DA 11 E DA 24 1_555 E N3 DT 6 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D N6 DA 11 E DA 24 1_555 E O4 DT 6 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N3 DC 12 E DC 25 1_555 E N1 DG 5 F DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N4 DC 12 E DC 25 1_555 E O6 DG 5 F DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D O2 DC 12 E DC 25 1_555 E N2 DG 5 F DG 4 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 70 n n N1 C6 CTP sing 71 n n N1 C1' CTP sing 72 n n C2 N3 CTP sing 73 n n C2 O2 CTP doub 74 n n N3 C4 CTP doub 75 n n C4 C5 CTP sing 76 n n C4 N4 CTP sing 77 n n C5 C6 CTP doub 78 n n C5 H5 CTP sing 79 n n C6 H6 CTP sing 80 n n N4 HN41 CTP sing 81 n n N4 HN42 CTP sing 82 n n C1' C2' CTP sing 83 n n C1' O4' CTP sing 84 n n C1' H1' CTP sing 85 n n C2' O2' CTP sing 86 n n C2' C3' CTP sing 87 n n C2' H2' CTP sing 88 n n O2' HO2' CTP sing 89 n n C3' C4' CTP sing 90 n n C3' O3' CTP sing 91 n n C3' H3' CTP sing 92 n n C4' O4' CTP sing 93 n n C4' C5' CTP sing 94 n n C4' H4' CTP sing 95 n n O3' HO3' CTP sing 96 n n C5' O5' CTP sing 97 n n C5' "H5'1" CTP sing 98 n n C5' "H5'2" CTP sing 99 n n O5' PA CTP sing 100 n n PA O1A CTP doub 101 n n PA O2A CTP sing 102 n n PA O3A CTP sing 103 n n O2A HOA2 CTP sing 104 n n O3A PB CTP sing 105 n n PB O1B CTP doub 106 n n PB O2B CTP sing 107 n n PB O3B CTP sing 108 n n O2B HOB2 CTP sing 109 n n O3B PG CTP sing 110 n n PG O1G CTP doub 111 n n PG O2G CTP sing 112 n n PG O3G CTP sing 113 n n O2G HOG2 CTP sing 114 n n O3G HOG3 CTP sing 115 n n # _atom_sites.entry_id 8K8U _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 F 6 MG A 1 1101 1 MG MG . G 6 MG A 1 1102 2 MG MG . H 6 MG A 1 1103 3 MG MG . I 7 CTP A 1 1104 1 CTP CTP . J 8 HOH A 1 1201 1 HOH HOH . J 8 HOH A 2 1202 2 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 . . . I 7 143.671 155.608 140.382 1 25.49 ? N1 CTP 1104 A 1 HETATM 2 C C2 CTP . . . I 7 144.118 154.313 140.257 1 27.08 ? C2 CTP 1104 A 1 HETATM 3 N N3 CTP . . . I 7 144.071 153.678 139.038 1 25.26 ? N3 CTP 1104 A 1 HETATM 4 C C4 CTP . . . I 7 143.621 154.354 137.93 1 25.21 ? C4 CTP 1104 A 1 HETATM 5 C C5 CTP . . . I 7 143.369 155.707 138.032 1 17.75 ? C5 CTP 1104 A 1 HETATM 6 C C6 CTP . . . I 7 143.147 156.233 139.293 1 29.5 ? C6 CTP 1104 A 1 HETATM 7 O O2 CTP . . . I 7 144.57 153.719 141.23 1 34.64 ? O2 CTP 1104 A 1 HETATM 8 N N4 CTP . . . I 7 143.435 153.716 136.783 1 33.01 ? N4 CTP 1104 A 1 HETATM 9 C C1' CTP . . . I 7 144.185 156.433 141.481 1 23.89 ? C1' CTP 1104 A 1 HETATM 10 C C2' CTP . . . I 7 145.643 156.751 141.199 1 28.87 ? C2' CTP 1104 A 1 HETATM 11 C C3' CTP . . . I 7 145.764 158.25 141.306 1 13.91 ? C3' CTP 1104 A 1 HETATM 12 C C4' CTP . . . I 7 144.4 158.71 141.773 1 31.14 ? C4' CTP 1104 A 1 HETATM 13 O O4' CTP . . . I 7 143.497 157.662 141.502 1 21.59 ? O4' CTP 1104 A 1 HETATM 14 O O3' CTP . . . I 7 146.742 158.592 142.25 1 35.46 ? O3' CTP 1104 A 1 HETATM 15 C C5' CTP . . . I 7 144.01 159.999 141.065 1 38.95 ? C5' CTP 1104 A 1 HETATM 16 O O5' CTP . . . I 7 143.199 159.784 139.936 1 39.36 ? O5' CTP 1104 A 1 HETATM 17 P PA CTP . . . I 7 143.601 160.401 138.511 1 23.49 ? PA CTP 1104 A 1 HETATM 18 O O1A CTP . . . I 7 143.42 161.889 138.549 1 29.3 ? O1A CTP 1104 A 1 HETATM 19 O O2A CTP . . . I 7 142.769 159.797 137.416 1 28.59 ? O2A CTP 1104 A 1 HETATM 20 O O3A CTP . . . I 7 145.157 160.032 138.358 1 41.83 ? O3A CTP 1104 A 1 HETATM 21 P PB CTP . . . I 7 146.334 161.125 138.411 1 30.79 ? PB CTP 1104 A 1 HETATM 22 O O1B CTP . . . I 7 146.03 162.143 139.476 1 27.2 ? O1B CTP 1104 A 1 HETATM 23 O O2B CTP . . . I 7 147.645 160.436 138.658 1 36.51 ? O2B CTP 1104 A 1 HETATM 24 O O3B CTP . . . I 7 146.35 161.793 136.951 1 28.47 ? O3B CTP 1104 A 1 HETATM 25 P PG CTP . . . I 7 146.719 163.328 136.665 1 38.42 ? PG CTP 1104 A 1 HETATM 26 O O1G CTP . . . I 7 145.592 163.935 135.874 1 40.84 ? O1G CTP 1104 A 1 HETATM 27 O O2G CTP . . . I 7 147.997 163.404 135.879 1 40.23 ? O2G CTP 1104 A 1 HETATM 28 O O3G CTP . . . I 7 146.878 164.093 137.948 1 35.68 ? O3G CTP 1104 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #