data_5JPT # _model_server_result.job_id by94sAXuISqt0Jr3KVAlkQ _model_server_result.datetime_utc '2025-03-21 14:45:49' _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 5jpt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":801}' # _entry.id 5JPT # _exptl.entry_id 5JPT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _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 5JPT _cell.length_a 118.07 _cell.length_b 118.07 _cell.length_c 252.15 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JPT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,J 1 1 B,H,I,K 2 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 ? 2 C N N ? 2 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 OG1 THR 123 A THR 123 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc2 A NE2 HIS 479 A HIS 479 1_555 G NI NI . A NI 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc3 C O3B CDP . A CDP 801 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc4 D MG MG . A MG 802 1_555 J O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc5 D MG MG . A MG 802 1_555 J O HOH . A HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 D MG MG . A MG 802 1_555 J O HOH . A HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc7 D MG MG . A MG 802 1_555 J O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc8 B OG1 THR 123 B THR 123 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc9 H O1B CDP . B CDP 801 1_555 I MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc10 I MG MG . B MG 802 1_555 K O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc11 I MG MG . B MG 802 1_555 K O HOH . B HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc12 I MG MG . B MG 802 1_555 K O HOH . B HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc13 I MG MG . B MG 802 1_555 K O HOH . B HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? # _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 76 n n PB O1B CDP doub 77 n n PB O2B CDP sing 78 n n PB O3A CDP sing 79 n n O3A PA CDP sing 80 n n PA O1A CDP doub 81 n n PA O2A CDP sing 82 n n PA O5' CDP sing 83 n n O5' C5' CDP sing 84 n n C5' C4' CDP sing 85 n n C5' "H5'1" CDP sing 86 n n C5' "H5'2" CDP sing 87 n n C4' O4' CDP sing 88 n n C4' C3' CDP sing 89 n n C4' H4' CDP sing 90 n n O4' C1' CDP sing 91 n n C3' O3' CDP sing 92 n n C3' C2' CDP sing 93 n n C3' H3' CDP sing 94 n n O3' HA CDP sing 95 n n C2' O2' CDP sing 96 n n C2' C1' CDP sing 97 n n C2' H2' CDP sing 98 n n O2' HB CDP sing 99 n n C1' N1 CDP sing 100 n n C1' H1' CDP sing 101 n n N1 C2 CDP sing 102 n n N1 C6 CDP sing 103 n n C2 O2 CDP doub 104 n n C2 N3 CDP sing 105 n n N3 C4 CDP doub 106 n n C4 N4 CDP sing 107 n n C4 C5 CDP sing 108 n n N4 H4N1 CDP sing 109 n n N4 H4N2 CDP sing 110 n n C5 C6 CDP doub 111 n n C5 H5 CDP sing 112 n n C6 H6 CDP sing 113 n n HO1 O2A CDP sing 114 n n HO2 O2B CDP sing 115 n n HO3 O3B CDP sing 116 n n # _atom_sites.entry_id 5JPT _atom_sites.fract_transf_matrix[1][1] 0.00847 _atom_sites.fract_transf_matrix[1][2] 0.00489 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00978 _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] 0.003966 _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 CDP A 1 801 1750 CDP CDP . D 3 MG A 1 802 1751 MG MG . E 4 GOL A 1 803 1752 GOL GOL . F 5 ACT A 1 804 1753 ACT ACT . G 6 NI A 1 805 1754 NI NI . H 2 CDP B 1 801 1750 CDP CDP . I 3 MG B 1 802 1751 MG MG . J 7 HOH A 1 901 1763 HOH HOH . J 7 HOH A 2 902 1764 HOH HOH . J 7 HOH A 3 903 1756 HOH HOH . J 7 HOH A 4 904 1759 HOH HOH . J 7 HOH A 5 905 1769 HOH HOH . J 7 HOH A 6 906 1768 HOH HOH . J 7 HOH A 7 907 1758 HOH HOH . J 7 HOH A 8 908 1762 HOH HOH . J 7 HOH A 9 909 1761 HOH HOH . J 7 HOH A 10 910 1755 HOH HOH . J 7 HOH A 11 911 1760 HOH HOH . J 7 HOH A 12 912 1767 HOH HOH . J 7 HOH A 13 913 1757 HOH HOH . J 7 HOH A 14 914 1765 HOH HOH . J 7 HOH A 15 915 1766 HOH HOH . K 7 HOH B 1 901 1758 HOH HOH . K 7 HOH B 2 902 1757 HOH HOH . K 7 HOH B 3 903 1760 HOH HOH . K 7 HOH B 4 904 1762 HOH HOH . K 7 HOH B 5 905 1759 HOH HOH . K 7 HOH B 6 906 1756 HOH HOH . K 7 HOH B 7 907 1761 HOH HOH . K 7 HOH B 8 908 1755 HOH HOH . K 7 HOH B 9 909 1752 HOH HOH . K 7 HOH B 10 910 1754 HOH HOH . K 7 HOH B 11 911 1753 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 2 -14.333 -26.53 30.712 1 36.58 ? O3B CDP 801 A 1 HETATM 2 P PB CDP . . . C 2 -14.329 -26.157 29.235 1 34.47 ? PB CDP 801 A 1 HETATM 3 O O1B CDP . . . C 2 -13.49 -27.165 28.462 1 34.88 ? O1B CDP 801 A 1 HETATM 4 O O2B CDP . . . C 2 -15.753 -26.178 28.705 1 38.12 -1 O2B CDP 801 A 1 HETATM 5 O O3A CDP . . . C 2 -13.719 -24.69 29.052 1 31.28 ? O3A CDP 801 A 1 HETATM 6 P PA CDP . . . C 2 -12.786 -23.976 30.161 1 39.5 ? PA CDP 801 A 1 HETATM 7 O O1A CDP . . . C 2 -11.59 -24.835 30.412 1 40.45 -1 O1A CDP 801 A 1 HETATM 8 O O2A CDP . . . C 2 -13.551 -23.777 31.444 1 32.89 ? O2A CDP 801 A 1 HETATM 9 O O5' CDP . . . C 2 -12.322 -22.576 29.615 1 41.2 ? O5' CDP 801 A 1 HETATM 10 C C5' CDP . . . C 2 -11.519 -22.553 28.455 1 43.64 ? C5' CDP 801 A 1 HETATM 11 C C4' CDP . . . C 2 -10.711 -21.275 28.447 1 41.98 ? C4' CDP 801 A 1 HETATM 12 O O4' CDP . . . C 2 -9.898 -21.158 29.829 1 39.15 ? O4' CDP 801 A 1 HETATM 13 C C3' CDP . . . C 2 -9.866 -21.292 27.472 1 41.95 ? C3' CDP 801 A 1 HETATM 14 O O3' CDP . . . C 2 -9.853 -19.964 26.794 1 51.4 ? O3' CDP 801 A 1 HETATM 15 C C2' CDP . . . C 2 -8.48 -21.572 28.095 1 42.69 ? C2' CDP 801 A 1 HETATM 16 O O2' CDP . . . C 2 -7.528 -20.75 27.538 1 44.86 ? O2' CDP 801 A 1 HETATM 17 C C1' CDP . . . C 2 -8.616 -21.253 29.57 1 45.97 ? C1' CDP 801 A 1 HETATM 18 N N1 CDP . . . C 2 -8.012 -22.351 30.363 1 42.94 ? N1 CDP 801 A 1 HETATM 19 C C2 CDP . . . C 2 -6.653 -22.244 30.879 1 42.79 ? C2 CDP 801 A 1 HETATM 20 O O2 CDP . . . C 2 -5.989 -21.243 30.669 1 47.95 ? O2 CDP 801 A 1 HETATM 21 N N3 CDP . . . C 2 -6.078 -23.354 31.661 1 41.4 ? N3 CDP 801 A 1 HETATM 22 C C4 CDP . . . C 2 -6.84 -24.527 31.915 1 39.9 ? C4 CDP 801 A 1 HETATM 23 N N4 CDP . . . C 2 -6.286 -25.582 32.663 1 41.51 ? N4 CDP 801 A 1 HETATM 24 C C5 CDP . . . C 2 -8.208 -24.64 31.397 1 42.79 ? C5 CDP 801 A 1 HETATM 25 C C6 CDP . . . C 2 -8.785 -23.531 30.614 1 43.33 ? C6 CDP 801 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #