data_1U40 # _model_server_result.job_id 9ymsvwPjORyoRI6gGhA6Vw _model_server_result.datetime_utc '2024-11-24 15:31:57' _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 1u40 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":669}' # _entry.id 1U40 # _exptl.entry_id 1U40 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.308 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL _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 1U40 _cell.length_a 144.81 _cell.length_b 144.81 _cell.length_c 144.81 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U40 _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 _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 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 OD1 ASP 8 A ASP 8 1_555 B ZN ZN . A ZN 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc2 A NE2 HIS 10 A HIS 10 1_555 B ZN ZN . A ZN 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc3 A ND1 HIS 42 A HIS 42 1_555 B ZN ZN . A ZN 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc4 B ZN ZN . A ZN 160 1_555 C O1B CDM . A CDM 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? # _chem_comp.formula 'C14 H25 N3 O14 P2' _chem_comp.formula_weight 521.308 _chem_comp.id CDM _chem_comp.mon_nstd_flag . _chem_comp.name 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL _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 CDM sing 70 n n N1 C6 CDM sing 71 n n N1 C1' CDM sing 72 n n C2 N3 CDM sing 73 n n C2 O2 CDM doub 74 n n N3 C4 CDM doub 75 n n C4 C5 CDM sing 76 n n C4 N4 CDM sing 77 n n C5 C6 CDM doub 78 n n C5 H5 CDM sing 79 n n C6 H6 CDM sing 80 n n N4 H41 CDM sing 81 n n N4 H42 CDM sing 82 n n C1' C2' CDM sing 83 n n C1' O4' CDM sing 84 n n C1' H1' CDM sing 85 n n C2' O2' CDM sing 86 n n C2' C3' CDM sing 87 n n C2' H2' CDM sing 88 n n O2' "HO'2" CDM sing 89 n n C3' C4' CDM sing 90 n n C3' O3' CDM sing 91 n n C3' H3' CDM sing 92 n n C4' O4' CDM sing 93 n n C4' C5' CDM sing 94 n n C4' H4' CDM sing 95 n n O3' H3T CDM sing 96 n n C5' O5' CDM sing 97 n n C5' "H5'1" CDM sing 98 n n C5' "H5'2" CDM sing 99 n n O5' PA CDM sing 100 n n PA O1A CDM doub 101 n n PA O2A CDM sing 102 n n PA O3A CDM sing 103 n n O2A HO2A CDM sing 104 n n O3A PB CDM sing 105 n n PB O1B CDM sing 106 n n PB O2B CDM doub 107 n n PB O3B CDM sing 108 n n O1B HO1B CDM sing 109 n n O3B C1M CDM sing 110 n n C1M C2M CDM sing 111 n n C1M H1M1 CDM sing 112 n n C1M H1M2 CDM sing 113 n n C2M O2M CDM sing 114 n n C2M C3M CDM sing 115 n n C2M H2M1 CDM sing 116 n n O2M H2M2 CDM sing 117 n n C3M C4M CDM sing 118 n n C3M C5M CDM sing 119 n n C3M O3M CDM sing 120 n n C4M O4M CDM sing 121 n n C4M H4M1 CDM sing 122 n n C4M H4M2 CDM sing 123 n n C5M H5M1 CDM sing 124 n n C5M H5M2 CDM sing 125 n n C5M H5M3 CDM sing 126 n n O3M H3M CDM sing 127 n n O4M H4M CDM sing 128 n n # _atom_sites.entry_id 1U40 _atom_sites.fract_transf_matrix[1][1] 0.006906 _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] 0.006906 _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] 0.006906 _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 ZN A 1 160 156 ZN ZN . C 3 CDM A 1 669 669 CDM SUB . # 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 CDM . . . C 3 8.512 30.521 12.641 1 34.81 ? N1 CDM 669 A 1 HETATM 2 C C2 CDM . . . C 3 7.404 30.61 13.395 1 35.06 ? C2 CDM 669 A 1 HETATM 3 N N3 CDM . . . C 3 6.724 29.477 13.678 1 33.19 ? N3 CDM 669 A 1 HETATM 4 C C4 CDM . . . C 3 7.117 28.284 13.237 1 30.19 ? C4 CDM 669 A 1 HETATM 5 C C5 CDM . . . C 3 8.331 28.194 12.419 1 29.3 ? C5 CDM 669 A 1 HETATM 6 C C6 CDM . . . C 3 8.97 29.334 12.161 1 31.06 ? C6 CDM 669 A 1 HETATM 7 O O2 CDM . . . C 3 7.012 31.682 13.821 1 37.83 ? O2 CDM 669 A 1 HETATM 8 N N4 CDM . . . C 3 6.389 27.217 13.562 1 29.45 ? N4 CDM 669 A 1 HETATM 9 C C1' CDM . . . C 3 9.27 31.736 12.314 1 39.26 ? C1' CDM 669 A 1 HETATM 10 C C2' CDM . . . C 3 10.512 32.023 13.152 1 44.03 ? C2' CDM 669 A 1 HETATM 11 O O2' CDM . . . C 3 10.305 33.151 14.018 1 50.7 ? O2' CDM 669 A 1 HETATM 12 C C3' CDM . . . C 3 11.651 32.24 12.149 1 44.36 ? C3' CDM 669 A 1 HETATM 13 C C4' CDM . . . C 3 10.987 32.244 10.754 1 42.71 ? C4' CDM 669 A 1 HETATM 14 O O4' CDM . . . C 3 9.678 31.693 10.926 1 39.67 ? O4' CDM 669 A 1 HETATM 15 O O3' CDM . . . C 3 12.253 33.51 12.342 1 46.07 ? O3' CDM 669 A 1 HETATM 16 C C5' CDM . . . C 3 11.869 31.442 9.714 1 45.27 ? C5' CDM 669 A 1 HETATM 17 O O5' CDM . . . C 3 11.44 30.076 9.471 1 50.96 ? O5' CDM 669 A 1 HETATM 18 P PA CDM . . . C 3 12.155 28.998 8.477 1 49.68 ? PA CDM 669 A 1 HETATM 19 O O1A CDM . . . C 3 11.881 27.525 9.034 1 53.26 ? O1A CDM 669 A 1 HETATM 20 O O2A CDM . . . C 3 11.541 29.133 7.002 1 55.8 ? O2A CDM 669 A 1 HETATM 21 O O3A CDM . . . C 3 13.758 29.217 8.557 1 59.44 ? O3A CDM 669 A 1 HETATM 22 P PB CDM . . . C 3 14.699 29.269 7.221 1 62.77 ? PB CDM 669 A 1 HETATM 23 O O1B CDM . . . C 3 16.173 28.784 7.652 1 58.86 ? O1B CDM 669 A 1 HETATM 24 O O2B CDM . . . C 3 14.191 28.335 6.019 1 63.75 ? O2B CDM 669 A 1 HETATM 25 O O3B CDM . . . C 3 14.788 30.775 6.696 1 67.21 ? O3B CDM 669 A 1 HETATM 26 C C1M CDM . . . C 3 15.216 31.821 7.568 1 71.79 ? C1M CDM 669 A 1 HETATM 27 C C2M CDM . . . C 3 15.158 33.136 6.741 1 73.86 ? C2M CDM 669 A 1 HETATM 28 O O2M CDM . . . C 3 15.56 34.235 7.57 1 78.73 ? O2M CDM 669 A 1 HETATM 29 C C3M CDM . . . C 3 16.061 33.211 5.457 1 74.19 ? C3M CDM 669 A 1 HETATM 30 C C4M CDM . . . C 3 15.597 34.476 4.643 1 74.4 ? C4M CDM 669 A 1 HETATM 31 C C5M CDM . . . C 3 17.563 33.361 5.828 1 72.22 ? C5M CDM 669 A 1 HETATM 32 O O3M CDM . . . C 3 15.895 32.07 4.562 1 74.9 ? O3M CDM 669 A 1 HETATM 33 O O4M CDM . . . C 3 16.37 34.642 3.439 1 76.36 ? O4M CDM 669 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #