data_9LJT # _model_server_result.job_id Gs3jdlA6cmCaQNjQ0HYHQw _model_server_result.datetime_utc '2025-08-15 03:01:01' _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 9ljt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 9LJT # _exptl.entry_id 9LJT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _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 9LJT _cell.length_a 139.843 _cell.length_b 139.843 _cell.length_c 92.651 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LJT _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 OD2 ASP 221 A ASP 220 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A OD1 ASP 221 A ASP 220 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc3 A O THR 222 A THR 221 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc4 A OD1 ASP 319 A ASP 318 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc5 A OD2 ASP 319 A ASP 318 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc6 A OD1 ASP 320 A ASP 319 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc7 C O2A CDP . A CDP 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc8 C O1B CDP . A CDP 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc9 C O2A CDP . A CDP 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _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 O3B PB CDP sing 70 n n PB O1B CDP doub 71 n n PB O2B CDP sing 72 n n PB O3A CDP sing 73 n n O3A PA CDP sing 74 n n PA O1A CDP doub 75 n n PA O2A CDP sing 76 n n PA O5' CDP sing 77 n n O5' C5' CDP sing 78 n n C5' C4' CDP sing 79 n n C5' "H5'1" CDP sing 80 n n C5' "H5'2" CDP sing 81 n n C4' O4' CDP sing 82 n n C4' C3' CDP sing 83 n n C4' H4' CDP sing 84 n n O4' C1' CDP sing 85 n n C3' O3' CDP sing 86 n n C3' C2' CDP sing 87 n n C3' H3' CDP sing 88 n n O3' HA CDP sing 89 n n C2' O2' CDP sing 90 n n C2' C1' CDP sing 91 n n C2' H2' CDP sing 92 n n O2' HB CDP sing 93 n n C1' N1 CDP sing 94 n n C1' H1' CDP sing 95 n n N1 C2 CDP sing 96 n n N1 C6 CDP sing 97 n n C2 O2 CDP doub 98 n n C2 N3 CDP sing 99 n n N3 C4 CDP doub 100 n n C4 N4 CDP sing 101 n n C4 C5 CDP sing 102 n n N4 H4N1 CDP sing 103 n n N4 H4N2 CDP sing 104 n n C5 C6 CDP doub 105 n n C5 H5 CDP sing 106 n n C6 H6 CDP sing 107 n n HO1 O2A CDP sing 108 n n HO2 O2B CDP sing 109 n n HO3 O3B CDP sing 110 n n # _atom_sites.entry_id 9LJT _atom_sites.fract_transf_matrix[1][1] 0.007151 _atom_sites.fract_transf_matrix[1][2] 0.004129 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008257 _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] 0.010793 _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 3 CDP A 1 601 602 CDP CDP . D 4 MN A 1 602 1 MN MN . E 4 MN A 1 603 2 MN MN . F 5 FAD T 1 601 601 FAD FAD . G 6 HOH A 1 701 33 HOH HOH . G 6 HOH A 2 702 64 HOH HOH . G 6 HOH A 3 703 29 HOH HOH . G 6 HOH A 4 704 86 HOH HOH . G 6 HOH A 5 705 34 HOH HOH . G 6 HOH A 6 706 10 HOH HOH . G 6 HOH A 7 707 106 HOH HOH . G 6 HOH A 8 708 14 HOH HOH . G 6 HOH A 9 709 43 HOH HOH . G 6 HOH A 10 710 126 HOH HOH . G 6 HOH A 11 711 109 HOH HOH . G 6 HOH A 12 712 5 HOH HOH . G 6 HOH A 13 713 76 HOH HOH . G 6 HOH A 14 714 36 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 O O3B CDP . . . C 3 40.905 -42.826 2.799 1 56.12 ? O3B CDP 601 A 1 HETATM 2 P PB CDP . . . C 3 42.242 -42.224 2.449 1 65.06 ? PB CDP 601 A 1 HETATM 3 O O1B CDP . . . C 3 42.72 -42.703 1.108 1 56.55 ? O1B CDP 601 A 1 HETATM 4 O O2B CDP . . . C 3 42.067 -40.72 2.49 1 58.1 ? O2B CDP 601 A 1 HETATM 5 O O3A CDP . . . C 3 43.406 -42.688 3.526 1 64.46 ? O3A CDP 601 A 1 HETATM 6 P PA CDP . . . C 3 43.858 -44.253 3.697 1 63.76 ? PA CDP 601 A 1 HETATM 7 O O1A CDP . . . C 3 44.458 -44.473 5.061 1 60.76 ? O1A CDP 601 A 1 HETATM 8 O O2A CDP . . . C 3 44.879 -44.586 2.655 1 57.93 ? O2A CDP 601 A 1 HETATM 9 O O5' CDP . . . C 3 42.479 -45.148 3.464 1 57.34 ? O5' CDP 601 A 1 HETATM 10 C C5' CDP . . . C 3 42.286 -46.296 4.256 1 59.76 ? C5' CDP 601 A 1 HETATM 11 C C4' CDP . . . C 3 40.835 -46.489 4.527 1 62.38 ? C4' CDP 601 A 1 HETATM 12 O O4' CDP . . . C 3 40.74 -47.112 5.671 1 68.48 ? O4' CDP 601 A 1 HETATM 13 C C3' CDP . . . C 3 39.993 -45.051 4.702 1 60.18 ? C3' CDP 601 A 1 HETATM 14 O O3' CDP . . . C 3 39.301 -44.622 3.476 1 59.13 ? O3' CDP 601 A 1 HETATM 15 C C2' CDP . . . C 3 39.133 -45.248 5.568 1 61.65 ? C2' CDP 601 A 1 HETATM 16 O O2' CDP . . . C 3 37.877 -45.842 4.981 1 55.27 ? O2' CDP 601 A 1 HETATM 17 C C1' CDP . . . C 3 39.807 -46.313 6.561 1 63.96 ? C1' CDP 601 A 1 HETATM 18 N N1 CDP . . . C 3 40.383 -45.71 7.593 1 59.92 ? N1 CDP 601 A 1 HETATM 19 C C2 CDP . . . C 3 39.627 -45.593 8.846 1 58.59 ? C2 CDP 601 A 1 HETATM 20 O O2 CDP . . . C 3 38.541 -46.039 8.891 1 59.68 ? O2 CDP 601 A 1 HETATM 21 N N3 CDP . . . C 3 40.228 -44.923 10.021 1 63.83 ? N3 CDP 601 A 1 HETATM 22 C C4 CDP . . . C 3 41.568 -44.378 9.961 1 65.4 ? C4 CDP 601 A 1 HETATM 23 N N4 CDP . . . C 3 42.179 -43.724 11.121 1 68.85 ? N4 CDP 601 A 1 HETATM 24 C C5 CDP . . . C 3 42.347 -44.482 8.711 1 66.07 ? C5 CDP 601 A 1 HETATM 25 C C6 CDP . . . C 3 41.725 -45.155 7.54 1 66.41 ? C6 CDP 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 554 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #