data_2DJH # _model_server_result.job_id asD-CYFZJTLkpVE5SOAXxw _model_server_result.datetime_utc '2024-10-19 16:34:49' _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 2djh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":118}' # _entry.id 2DJH # _exptl.entry_id 2DJH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 3'-MONOPHOSPHATE" _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 2DJH _cell.length_a 29.19 _cell.length_b 48.72 _cell.length_c 62.58 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DJH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id P _struct_conn.ptnr1_label_comp_id 3PD _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id 3PD _struct_conn.ptnr1_auth_seq_id 117 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id O5' _struct_conn.ptnr2_label_comp_id UM3 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id UM3 _struct_conn.ptnr2_auth_seq_id 118 _struct_conn.ptnr2_symmetry 1_555 _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 1.595 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UM3 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 3'-MONOPHOSPHATE" _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 UM3 sing 363 n y N1 C6 UM3 sing 364 n y N1 C1' UM3 sing 365 n n C2 N3 UM3 sing 366 n y C2 O2 UM3 doub 367 n n N3 C4 UM3 sing 368 n y N3 HN3 UM3 sing 369 n n C4 C5 UM3 sing 370 n y C4 O4 UM3 doub 371 n n C5 C6 UM3 doub 372 n y C5 H5 UM3 sing 373 n n C6 H6 UM3 sing 374 n n C1' C2' UM3 sing 375 n n C1' O4' UM3 sing 376 n n C1' H1' UM3 sing 377 n n C2' C3' UM3 sing 378 n n C2' "H2'1" UM3 sing 379 n n C2' "H2'2" UM3 sing 380 n n C3' C4' UM3 sing 381 n n C3' O3' UM3 sing 382 n n C3' H3' UM3 sing 383 n n C4' O4' UM3 sing 384 n n C4' C5' UM3 sing 385 n n C4' H4' UM3 sing 386 n n O3' P UM3 sing 387 n n C5' O5' UM3 sing 388 n n C5' "H5'1" UM3 sing 389 n n C5' "H5'2" UM3 sing 390 n n O5' HO5' UM3 sing 391 n n P O1P UM3 doub 392 n n P O2P UM3 sing 393 n n P O3P UM3 sing 394 n n O2P HOP2 UM3 sing 395 n n O3P HOP3 UM3 sing 396 n n # _atom_sites.entry_id 2DJH _atom_sites.fract_transf_matrix[1][1] 0.034258 _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] 0.020525 _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] 0.01598 _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 3PD A 1 117 1 3PD GU . C 3 UM3 A 1 118 1 UM3 GU . D 4 HOH A 1 119 1 HOH TIP . D 4 HOH A 2 120 2 HOH TIP . D 4 HOH A 3 121 3 HOH TIP . D 4 HOH A 4 122 4 HOH TIP . D 4 HOH A 5 123 5 HOH TIP . D 4 HOH A 6 124 6 HOH TIP . D 4 HOH A 7 125 7 HOH TIP . D 4 HOH A 8 126 8 HOH TIP . D 4 HOH A 9 127 9 HOH TIP . D 4 HOH A 10 128 11 HOH TIP . D 4 HOH A 11 129 12 HOH TIP . D 4 HOH A 12 130 13 HOH TIP . D 4 HOH A 13 131 14 HOH TIP . D 4 HOH A 14 132 15 HOH TIP . D 4 HOH A 15 133 16 HOH TIP . D 4 HOH A 16 134 17 HOH TIP . D 4 HOH A 17 135 18 HOH TIP . D 4 HOH A 18 136 19 HOH TIP . D 4 HOH A 19 137 21 HOH TIP . D 4 HOH A 20 138 22 HOH TIP . D 4 HOH A 21 139 23 HOH TIP . D 4 HOH A 22 140 24 HOH TIP . D 4 HOH A 23 141 25 HOH TIP . D 4 HOH A 24 142 26 HOH TIP . D 4 HOH A 25 143 27 HOH TIP . D 4 HOH A 26 144 28 HOH TIP . D 4 HOH A 27 145 29 HOH TIP . D 4 HOH A 28 146 30 HOH TIP . D 4 HOH A 29 147 31 HOH TIP . D 4 HOH A 30 148 32 HOH TIP . D 4 HOH A 31 149 33 HOH TIP . D 4 HOH A 32 150 34 HOH TIP . D 4 HOH A 33 151 35 HOH TIP . D 4 HOH A 34 152 36 HOH TIP . D 4 HOH A 35 153 37 HOH TIP . D 4 HOH A 36 154 38 HOH TIP . D 4 HOH A 37 155 39 HOH TIP . D 4 HOH A 38 156 40 HOH TIP . D 4 HOH A 39 157 41 HOH TIP . D 4 HOH A 40 158 42 HOH TIP . D 4 HOH A 41 159 43 HOH TIP . D 4 HOH A 42 160 44 HOH TIP . D 4 HOH A 43 161 45 HOH TIP . D 4 HOH A 44 162 46 HOH TIP . D 4 HOH A 45 163 47 HOH TIP . D 4 HOH A 46 164 48 HOH TIP . D 4 HOH A 47 165 49 HOH TIP . D 4 HOH A 48 166 50 HOH TIP . D 4 HOH A 49 167 51 HOH TIP . D 4 HOH A 50 168 52 HOH TIP . D 4 HOH A 51 169 53 HOH TIP . D 4 HOH A 52 170 54 HOH TIP . D 4 HOH A 53 171 55 HOH TIP . D 4 HOH A 54 172 56 HOH TIP . D 4 HOH A 55 173 57 HOH TIP . D 4 HOH A 56 174 58 HOH TIP . D 4 HOH A 57 175 59 HOH TIP . D 4 HOH A 58 176 60 HOH TIP . D 4 HOH A 59 177 61 HOH TIP . D 4 HOH A 60 178 62 HOH TIP . D 4 HOH A 61 179 63 HOH TIP . D 4 HOH A 62 180 64 HOH TIP . D 4 HOH A 63 181 65 HOH TIP . D 4 HOH A 64 182 66 HOH TIP . D 4 HOH A 65 183 67 HOH TIP . D 4 HOH A 66 184 68 HOH TIP . D 4 HOH A 67 185 69 HOH TIP . D 4 HOH A 68 186 70 HOH TIP . D 4 HOH A 69 187 71 HOH TIP . D 4 HOH A 70 188 72 HOH TIP . D 4 HOH A 71 189 73 HOH TIP . D 4 HOH A 72 190 75 HOH TIP . D 4 HOH A 73 191 76 HOH TIP . D 4 HOH A 74 192 77 HOH TIP . D 4 HOH A 75 193 78 HOH TIP . D 4 HOH A 76 194 79 HOH TIP . D 4 HOH A 77 195 80 HOH TIP . D 4 HOH A 78 196 81 HOH TIP . D 4 HOH A 79 197 82 HOH TIP . D 4 HOH A 80 198 83 HOH TIP . D 4 HOH A 81 199 84 HOH TIP . D 4 HOH A 82 200 85 HOH TIP . D 4 HOH A 83 201 86 HOH TIP . D 4 HOH A 84 202 87 HOH TIP . D 4 HOH A 85 203 88 HOH TIP . D 4 HOH A 86 204 89 HOH TIP . D 4 HOH A 87 205 90 HOH TIP . D 4 HOH A 88 206 91 HOH TIP . D 4 HOH A 89 207 92 HOH TIP . D 4 HOH A 90 208 93 HOH TIP . D 4 HOH A 91 209 94 HOH TIP . D 4 HOH A 92 210 95 HOH TIP . D 4 HOH A 93 211 96 HOH TIP . D 4 HOH A 94 212 97 HOH TIP . D 4 HOH A 95 213 98 HOH TIP . D 4 HOH A 96 214 99 HOH TIP . D 4 HOH A 97 215 100 HOH TIP . D 4 HOH A 98 216 101 HOH TIP . D 4 HOH A 99 217 102 HOH TIP . D 4 HOH A 100 218 103 HOH TIP . D 4 HOH A 101 219 104 HOH TIP . D 4 HOH A 102 220 105 HOH TIP . D 4 HOH A 103 221 106 HOH TIP . D 4 HOH A 104 222 107 HOH TIP . D 4 HOH A 105 223 108 HOH TIP . # 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 UM3 . . . C 3 6.033 13.675 5.03 1 17.91 ? N1 UM3 118 A 1 HETATM 2 C C2 UM3 . . . C 3 4.754 13.053 5.134 1 16.77 ? C2 UM3 118 A 1 HETATM 3 N N3 UM3 . . . C 3 3.692 13.795 4.581 1 16.09 ? N3 UM3 118 A 1 HETATM 4 C C4 UM3 . . . C 3 3.776 15.049 3.959 1 15.19 ? C4 UM3 118 A 1 HETATM 5 C C5 UM3 . . . C 3 5.124 15.624 3.886 1 13.77 ? C5 UM3 118 A 1 HETATM 6 C C6 UM3 . . . C 3 6.193 14.941 4.41 1 16.18 ? C6 UM3 118 A 1 HETATM 7 O O2 UM3 . . . C 3 4.566 11.963 5.663 1 15.68 ? O2 UM3 118 A 1 HETATM 8 O O4 UM3 . . . C 3 2.761 15.581 3.526 1 17.04 ? O4 UM3 118 A 1 HETATM 9 C C1' UM3 . . . C 3 7.19 12.885 5.649 1 17.51 ? C1' UM3 118 A 1 HETATM 10 C C2' UM3 . . . C 3 8.35 12.444 4.757 1 19.74 ? C2' UM3 118 A 1 HETATM 11 C C3' UM3 . . . C 3 9.548 12.561 5.74 1 20.51 ? C3' UM3 118 A 1 HETATM 12 C C4' UM3 . . . C 3 9.149 13.801 6.555 1 19.82 ? C4' UM3 118 A 1 HETATM 13 O O3' UM3 . . . C 3 9.617 11.451 6.674 1 23.8 ? O3' UM3 118 A 1 HETATM 14 O O4' UM3 . . . C 3 7.712 13.694 6.677 1 17.62 ? O4' UM3 118 A 1 HETATM 15 C C5' UM3 . . . C 3 9.608 15.123 6.009 1 20.98 ? C5' UM3 118 A 1 HETATM 16 O O5' UM3 . . . C 3 10.947 15.342 6.489 1 23.93 ? O5' UM3 118 A 1 HETATM 17 P P UM3 . . . C 3 10.067 10.097 6.074 1 27.87 ? P UM3 118 A 1 HETATM 18 O O1P UM3 . . . C 3 10.09 9.143 7.131 1 25.36 ? O1P UM3 118 A 1 HETATM 19 O O2P UM3 . . . C 3 11.377 10.239 5.518 1 25.96 ? O2P UM3 118 A 1 HETATM 20 O O3P UM3 . . . C 3 9.165 9.624 5.064 1 29.45 ? O3P UM3 118 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #