data_1U3L # _model_server_result.job_id QjXApg9LAosNbKz6trR7Qw _model_server_result.datetime_utc '2024-11-24 15:35:07' _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 1u3l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":669}' # _entry.id 1U3L # _exptl.entry_id 1U3L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 4 _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 90 _cell.entry_id 1U3L _cell.length_a 144.66 _cell.length_b 144.66 _cell.length_c 144.66 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U3L _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 8 A ASP 8 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc2 A NE2 HIS 10 A HIS 10 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 A ND1 HIS 42 A HIS 42 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc4 A OE2 GLU 135 A GLU 135 5_555 B MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc5 D O2A CDP . A CDP 669 1_555 B MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc6 D O1B CDP . A CDP 669 1_555 B MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc7 D O2B CDP . A CDP 669 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? # _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 1U3L _atom_sites.fract_transf_matrix[1][1] 0.006913 _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] 0.006913 _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] 0.006913 _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 B 2 MG A 1 700 700 MG MG . C 3 ZN A 1 701 156 ZN ZN . D 4 CDP A 1 669 669 CDP CDP . # 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 . . . D 4 14.649 30.931 7.18 1 42.04 ? O3B CDP 669 A 1 HETATM 2 P PB CDP . . . D 4 14.479 29.278 7.006 1 34 ? PB CDP 669 A 1 HETATM 3 O O1B CDP . . . D 4 13.762 28.981 5.588 1 43.45 ? O1B CDP 669 A 1 HETATM 4 O O2B CDP . . . D 4 15.86 28.582 7.073 1 34.07 ? O2B CDP 669 A 1 HETATM 5 O O3A CDP . . . D 4 13.607 28.683 8.308 1 37.96 ? O3A CDP 669 A 1 HETATM 6 P PA CDP . . . D 4 11.976 28.573 8.2 1 32.45 ? PA CDP 669 A 1 HETATM 7 O O1A CDP . . . D 4 11.485 27.486 9.152 1 34.55 ? O1A CDP 669 A 1 HETATM 8 O O2A CDP . . . D 4 11.518 28.353 6.719 1 42.8 ? O2A CDP 669 A 1 HETATM 9 O O5' CDP . . . D 4 11.3 29.973 8.578 1 34.24 ? O5' CDP 669 A 1 HETATM 10 C C5' CDP . . . D 4 10.952 30.15 9.873 1 34.19 ? C5' CDP 669 A 1 HETATM 11 C C4' CDP . . . D 4 10.884 31.537 10.22 1 31.39 ? C4' CDP 669 A 1 HETATM 12 O O4' CDP . . . D 4 9.635 32.019 10.681 1 30.34 ? O4' CDP 669 A 1 HETATM 13 C C3' CDP . . . D 4 11.782 31.485 11.43 1 33.34 ? C3' CDP 669 A 1 HETATM 14 O O3' CDP . . . D 4 12.903 32.274 11.102 1 36.84 ? O3' CDP 669 A 1 HETATM 15 C C2' CDP . . . D 4 10.949 32.015 12.552 1 31.97 ? C2' CDP 669 A 1 HETATM 16 O O2' CDP . . . D 4 11.191 33.371 12.818 1 32.98 ? O2' CDP 669 A 1 HETATM 17 C C1' CDP . . . D 4 9.535 31.902 12.073 1 28.43 ? C1' CDP 669 A 1 HETATM 18 N N1 CDP . . . D 4 8.765 30.671 12.49 1 27.96 ? N1 CDP 669 A 1 HETATM 19 C C2 CDP . . . D 4 7.666 30.747 13.343 1 27.87 ? C2 CDP 669 A 1 HETATM 20 O O2 CDP . . . D 4 7.283 31.831 13.803 1 32.85 ? O2 CDP 669 A 1 HETATM 21 N N3 CDP . . . D 4 6.934 29.67 13.731 1 26 ? N3 CDP 669 A 1 HETATM 22 C C4 CDP . . . D 4 7.264 28.449 13.288 1 22.26 ? C4 CDP 669 A 1 HETATM 23 N N4 CDP . . . D 4 6.526 27.405 13.686 1 20.28 ? N4 CDP 669 A 1 HETATM 24 C C5 CDP . . . D 4 8.355 28.298 12.437 1 22.12 ? C5 CDP 669 A 1 HETATM 25 C C6 CDP . . . D 4 9.063 29.436 12.072 1 25.79 ? C6 CDP 669 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #