data_4QJI # _model_server_result.job_id fONNh2Y9pcuqeSxLn43dwA _model_server_result.datetime_utc '2025-01-02 22:25:35' _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 4qji # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 4QJI # _exptl.entry_id 4QJI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 2 _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 4QJI _cell.length_a 90.58 _cell.length_b 90.58 _cell.length_c 109.57 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QJI _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,C,D,G 3 1 B,E,F,H 3 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_565 -x,-y+1,z+1/2 -1 0 0 0 -1 0 0 0 1 -45.29 78.444581 54.785 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 OD2 ASP 104 A ASP 281 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc2 A OD1 ASP 104 A ASP 281 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc3 C O2B CTP . A CTP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc4 C O1A CTP . A CTP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc5 C O1G CTP . A CTP 500 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc6 D MG MG . A MG 501 1_555 G O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc7 B OD2 ASP 104 B ASP 281 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc8 B OD1 ASP 104 B ASP 281 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc9 E O1A CTP . B CTP 500 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc10 E O1G CTP . B CTP 500 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc11 E O2B CTP . B CTP 500 1_555 F MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc12 F MG MG . B MG 501 1_555 H O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? # _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 4QJI _atom_sites.fract_transf_matrix[1][1] 0.01104 _atom_sites.fract_transf_matrix[1][2] 0.006374 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012748 _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] 0.009127 _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 CTP A 1 500 500 CTP CTP . D 3 MG A 1 501 501 MG MG . E 2 CTP B 1 500 500 CTP CTP . F 3 MG B 1 501 501 MG MG . G 4 HOH A 1 601 3 HOH HOH . G 4 HOH A 2 602 4 HOH HOH . G 4 HOH A 3 603 5 HOH HOH . G 4 HOH A 4 604 6 HOH HOH . G 4 HOH A 5 605 7 HOH HOH . G 4 HOH A 6 606 8 HOH HOH . G 4 HOH A 7 607 9 HOH HOH . G 4 HOH A 8 608 10 HOH HOH . G 4 HOH A 9 609 11 HOH HOH . G 4 HOH A 10 610 14 HOH HOH . G 4 HOH A 11 611 15 HOH HOH . G 4 HOH A 12 612 21 HOH HOH . G 4 HOH A 13 613 22 HOH HOH . H 4 HOH B 1 601 1 HOH HOH . H 4 HOH B 2 602 2 HOH HOH . H 4 HOH B 3 603 12 HOH HOH . H 4 HOH B 4 604 13 HOH HOH . H 4 HOH B 5 605 16 HOH HOH . H 4 HOH B 6 606 18 HOH HOH . H 4 HOH B 7 607 19 HOH HOH . H 4 HOH B 8 608 20 HOH HOH . H 4 HOH B 9 609 24 HOH HOH . H 4 HOH B 10 610 25 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 . . . C 2 -16.779 34.184 -2.008 1 44.38 ? N1 CTP 500 A 1 HETATM 2 C C2 CTP . . . C 2 -15.63 34.934 -2.146 1 47.26 ? C2 CTP 500 A 1 HETATM 3 N N3 CTP . . . C 2 -15.562 36.204 -1.61 1 48.66 ? N3 CTP 500 A 1 HETATM 4 C C4 CTP . . . C 2 -16.624 36.699 -0.884 1 49.62 ? C4 CTP 500 A 1 HETATM 5 C C5 CTP . . . C 2 -17.787 35.946 -0.766 1 48.42 ? C5 CTP 500 A 1 HETATM 6 C C6 CTP . . . C 2 -17.898 34.753 -1.472 1 47.57 ? C6 CTP 500 A 1 HETATM 7 O O2 CTP . . . C 2 -14.669 34.464 -2.752 1 50.7 ? O2 CTP 500 A 1 HETATM 8 N N4 CTP . . . C 2 -16.535 37.891 -0.302 1 53.71 ? N4 CTP 500 A 1 HETATM 9 C C1' CTP . . . C 2 -16.876 32.913 -2.746 1 45.16 ? C1' CTP 500 A 1 HETATM 10 C C2' CTP . . . C 2 -17.141 31.764 -1.788 1 40.89 ? C2' CTP 500 A 1 HETATM 11 O O2' CTP . . . C 2 -15.955 31.066 -1.496 1 40.56 ? O2' CTP 500 A 1 HETATM 12 C C3' CTP . . . C 2 -18.109 30.874 -2.532 1 42.3 ? C3' CTP 500 A 1 HETATM 13 C C4' CTP . . . C 2 -18.695 31.749 -3.627 1 44.44 ? C4' CTP 500 A 1 HETATM 14 O O4' CTP . . . C 2 -17.955 32.954 -3.657 1 48.94 ? O4' CTP 500 A 1 HETATM 15 O O3' CTP . . . C 2 -17.421 29.797 -3.124 1 43.59 ? O3' CTP 500 A 1 HETATM 16 C C5' CTP . . . C 2 -20.152 32.097 -3.367 1 43.23 ? C5' CTP 500 A 1 HETATM 17 O O5' CTP . . . C 2 -20.4 32.165 -1.981 1 46.99 ? O5' CTP 500 A 1 HETATM 18 P PA CTP . . . C 2 -21.707 32.96 -1.488 1 52.19 ? PA CTP 500 A 1 HETATM 19 O O1A CTP . . . C 2 -21.46 33.573 -0.129 1 45.96 ? O1A CTP 500 A 1 HETATM 20 O O2A CTP . . . C 2 -22.917 32.057 -1.473 1 53.31 ? O2A CTP 500 A 1 HETATM 21 O O3A CTP . . . C 2 -21.825 34.087 -2.636 1 65.51 ? O3A CTP 500 A 1 HETATM 22 P PB CTP . . . C 2 -22.217 35.621 -2.335 1 52.33 ? PB CTP 500 A 1 HETATM 23 O O1B CTP . . . C 2 -21.692 36.489 -3.452 1 54.55 ? O1B CTP 500 A 1 HETATM 24 O O2B CTP . . . C 2 -21.693 36.1 -1.002 1 48.51 ? O2B CTP 500 A 1 HETATM 25 O O3B CTP . . . C 2 -23.826 35.566 -2.368 1 68.99 ? O3B CTP 500 A 1 HETATM 26 P PG CTP . . . C 2 -24.724 35.95 -1.088 1 71.71 ? PG CTP 500 A 1 HETATM 27 O O1G CTP . . . C 2 -24.137 35.267 0.124 1 68.17 ? O1G CTP 500 A 1 HETATM 28 O O2G CTP . . . C 2 -24.761 37.445 -0.887 1 74.04 ? O2G CTP 500 A 1 HETATM 29 O O3G CTP . . . C 2 -26.126 35.437 -1.311 1 72.7 ? O3G CTP 500 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #