data_1MIY # _model_server_result.job_id eENnIn_JbiwkYBwkREjMsw _model_server_result.datetime_utc '2024-10-18 19:29:33' _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 1miy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":6501}' # _entry.id 1MIY # _exptl.entry_id 1MIY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 1MIY _cell.length_a 105.552 _cell.length_b 105.552 _cell.length_c 182.745 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MIY _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N 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 O ALA 77 A ALA 77 1_555 D MG MG . A MG 5611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc2 E O1A CTP . A CTP 5501 1_555 C MG MG . A MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc3 E O3A CTP . A CTP 5501 1_555 C MG MG . A MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc4 E O1G CTP . A CTP 5501 1_555 C MG MG . A MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc5 D MG MG . A MG 5611 1_555 I O HOH . A HOH 5612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 D MG MG . A MG 5611 1_555 B NZ LYS 58 B LYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.142 ? metalc ? metalc7 B O ALA 77 B ALA 77 1_555 G MG MG . B MG 6611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc8 H O1G CTP . B CTP 6501 1_555 F MG MG . B MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.051 ? metalc ? metalc9 H O3A CTP . B CTP 6501 1_555 F MG MG . B MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc10 H O1A CTP . B CTP 6501 1_555 F MG MG . B MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc11 G MG MG . B MG 6611 1_555 J O HOH . B HOH 6612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? # _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 1MIY _atom_sites.fract_transf_matrix[1][1] 0.009474 _atom_sites.fract_transf_matrix[1][2] 0.00547 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01094 _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] 0.005472 _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 C 2 MG A 1 5601 5601 MG MG . D 2 MG A 1 5611 5611 MG MG . E 3 CTP A 1 5501 5501 CTP CTP . F 2 MG B 1 6601 6601 MG MG . G 2 MG B 1 6611 6611 MG MG . H 3 CTP B 1 6501 6501 CTP CTP . I 4 HOH A 1 5602 5602 HOH HOH . I 4 HOH A 2 5612 5612 HOH HOH . I 4 HOH A 3 5613 5613 HOH HOH . I 4 HOH A 4 5703 5703 HOH HOH . I 4 HOH A 5 5704 5704 HOH HOH . I 4 HOH A 6 5706 5706 HOH HOH . I 4 HOH A 7 5707 5707 HOH HOH . I 4 HOH A 8 5801 5801 HOH HOH . I 4 HOH A 9 5802 5802 HOH HOH . I 4 HOH A 10 5803 5803 HOH HOH . I 4 HOH A 11 5804 5804 HOH HOH . I 4 HOH A 12 5805 5805 HOH HOH . I 4 HOH A 13 5806 5806 HOH HOH . I 4 HOH A 14 5807 5807 HOH HOH . I 4 HOH A 15 5901 5901 HOH HOH . I 4 HOH A 16 5902 5902 HOH HOH . I 4 HOH A 17 6614 6614 HOH HOH . J 4 HOH B 1 5614 5614 HOH HOH . J 4 HOH B 2 6602 6602 HOH HOH . J 4 HOH B 3 6612 6612 HOH HOH . J 4 HOH B 4 6613 6613 HOH HOH . J 4 HOH B 5 6703 6703 HOH HOH . J 4 HOH B 6 6704 6704 HOH HOH . J 4 HOH B 7 6706 6706 HOH HOH . J 4 HOH B 8 6707 6707 HOH HOH . J 4 HOH B 9 6801 6801 HOH HOH . J 4 HOH B 10 6802 6802 HOH HOH . J 4 HOH B 11 6803 6803 HOH HOH . J 4 HOH B 12 6804 6804 HOH HOH . J 4 HOH B 13 6805 6805 HOH HOH . J 4 HOH B 14 6806 6806 HOH HOH . J 4 HOH B 15 6807 6807 HOH HOH . J 4 HOH B 16 6901 6901 HOH HOH . J 4 HOH B 17 6902 6902 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 . . . H 3 24.052 43.949 56.75 1 25.33 ? N1 CTP 6501 B 1 HETATM 2 C C2 CTP . . . H 3 24.032 45.348 56.722 1 25.33 ? C2 CTP 6501 B 1 HETATM 3 N N3 CTP . . . H 3 22.993 46.035 57.302 1 25.33 ? N3 CTP 6501 B 1 HETATM 4 C C4 CTP . . . H 3 21.973 45.353 57.917 1 25.33 ? C4 CTP 6501 B 1 HETATM 5 C C5 CTP . . . H 3 21.946 43.96 57.923 1 25.33 ? C5 CTP 6501 B 1 HETATM 6 C C6 CTP . . . H 3 23.008 43.273 57.342 1 25.33 ? C6 CTP 6501 B 1 HETATM 7 O O2 CTP . . . H 3 24.933 46.023 56.189 1 25.33 ? O2 CTP 6501 B 1 HETATM 8 N N4 CTP . . . H 3 21.022 46.067 58.499 1 25.33 ? N4 CTP 6501 B 1 HETATM 9 C C1' CTP . . . H 3 25.124 43.229 55.982 1 29.12 ? C1' CTP 6501 B 1 HETATM 10 C C2' CTP . . . H 3 26.32 42.753 56.823 1 29.07 ? C2' CTP 6501 B 1 HETATM 11 O O2' CTP . . . H 3 27.391 43.677 56.716 1 29.16 ? O2' CTP 6501 B 1 HETATM 12 C C3' CTP . . . H 3 26.65 41.356 56.284 1 28.42 ? C3' CTP 6501 B 1 HETATM 13 C C4' CTP . . . H 3 25.601 41.089 55.206 1 27.35 ? C4' CTP 6501 B 1 HETATM 14 O O4' CTP . . . H 3 24.651 42.149 55.185 1 27.76 ? O4' CTP 6501 B 1 HETATM 15 O O3' CTP . . . H 3 27.962 41.142 55.775 1 28.74 ? O3' CTP 6501 B 1 HETATM 16 C C5' CTP . . . H 3 24.894 39.763 55.48 1 27.36 ? C5' CTP 6501 B 1 HETATM 17 O O5' CTP . . . H 3 23.866 39.921 56.46 1 24.67 ? O5' CTP 6501 B 1 HETATM 18 P PA CTP . . . H 3 23.535 38.822 57.641 1 23.93 ? PA CTP 6501 B 1 HETATM 19 O O1A CTP . . . H 3 22.55 37.846 57.084 1 28.96 ? O1A CTP 6501 B 1 HETATM 20 O O2A CTP . . . H 3 22.917 39.456 58.928 1 22.13 ? O2A CTP 6501 B 1 HETATM 21 O O3A CTP . . . H 3 25.021 38.164 57.928 1 23.81 ? O3A CTP 6501 B 1 HETATM 22 P PB CTP . . . H 3 26.233 38.793 58.868 1 22.86 ? PB CTP 6501 B 1 HETATM 23 O O1B CTP . . . H 3 25.871 40.173 59.332 1 24.34 ? O1B CTP 6501 B 1 HETATM 24 O O2B CTP . . . H 3 27.606 38.847 58.136 1 26.58 ? O2B CTP 6501 B 1 HETATM 25 O O3B CTP . . . H 3 26.235 37.777 60.139 1 22.78 ? O3B CTP 6501 B 1 HETATM 26 P PG CTP . . . H 3 25.081 36.613 60.266 1 19.54 ? PG CTP 6501 B 1 HETATM 27 O O1G CTP . . . H 3 25.388 35.646 59.026 1 24.01 ? O1G CTP 6501 B 1 HETATM 28 O O2G CTP . . . H 3 25.238 35.836 61.664 1 21.14 ? O2G CTP 6501 B 1 HETATM 29 O O3G CTP . . . H 3 23.561 37.157 60.219 1 21.16 ? O3G CTP 6501 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 29 #