data_6J5V # _model_server_result.job_id ThiiadVwKRHs3Q5ZWxIQVw _model_server_result.datetime_utc '2025-09-04 02:31:24' _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 6j5v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6J5V # _exptl.entry_id 6J5V _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 90 _cell.entry_id 6J5V _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J5V _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 ? _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 ? 4 D N N ? 4 E 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 covale ? covale1 B OG SER 253 C SER 253 1_555 E P U5P . C U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale2 B OG1 THR 254 C THR 254 1_555 D P U5P . C U5P 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.649 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-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 U5P sing 356 n n N1 C6 U5P sing 357 n n N1 C1' U5P sing 358 n n C2 N3 U5P sing 359 n n C2 O2 U5P doub 360 n n N3 C4 U5P sing 361 n n N3 HN3 U5P sing 362 n n C4 C5 U5P sing 363 n n C4 O4 U5P doub 364 n n C5 C6 U5P doub 365 n n C5 H5 U5P sing 366 n n C6 H6 U5P sing 367 n n C1' C2' U5P sing 368 n n C1' O4' U5P sing 369 n n C1' H1' U5P sing 370 n n C2' O2' U5P sing 371 n n C2' C3' U5P sing 372 n n C2' H2' U5P sing 373 n n O2' HO2' U5P sing 374 n n C3' C4' U5P sing 375 n n C3' O3' U5P sing 376 n n C3' H3' U5P sing 377 n n C4' O4' U5P sing 378 n n C4' C5' U5P sing 379 n n C4' H4' U5P sing 380 n n O3' HO3' U5P sing 381 n n C5' O5' U5P sing 382 n n C5' "H5'1" U5P sing 383 n n C5' "H5'2" U5P sing 384 n n O5' P U5P sing 385 n n P O1P U5P doub 386 n n P O2P U5P sing 387 n n P O3P U5P sing 388 n n O2P HOP2 U5P sing 389 n n O3P HOP3 U5P sing 390 n n # _atom_sites.entry_id 6J5V _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 U5P C 1 501 1 U5P U5P . E 4 U5P C 1 502 2 U5P U5P . # 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 U5P . . . D 4 109.328 88.143 67.526 1 121.7 ? N1 U5P 501 C 1 HETATM 2 C C2 U5P . . . D 4 110.665 88.195 67.346 1 121.7 ? C2 U5P 501 C 1 HETATM 3 N N3 U5P . . . D 4 111.173 88.925 66.327 1 121.7 ? N3 U5P 501 C 1 HETATM 4 C C4 U5P . . . D 4 110.36 89.584 65.517 1 121.7 ? C4 U5P 501 C 1 HETATM 5 C C5 U5P . . . D 4 109.016 89.533 65.703 1 121.7 ? C5 U5P 501 C 1 HETATM 6 C C6 U5P . . . D 4 108.51 88.801 66.724 1 121.7 ? C6 U5P 501 C 1 HETATM 7 O O2 U5P . . . D 4 111.384 87.601 68.076 1 121.7 ? O2 U5P 501 C 1 HETATM 8 O O4 U5P . . . D 4 110.809 90.223 64.628 1 121.7 ? O4 U5P 501 C 1 HETATM 9 C C1' U5P . . . D 4 108.804 87.383 68.592 1 121.7 ? C1' U5P 501 C 1 HETATM 10 C C2' U5P . . . D 4 108.223 88.328 69.577 1 121.7 ? C2' U5P 501 C 1 HETATM 11 O O2' U5P . . . D 4 108.845 88.131 70.857 1 121.7 ? O2' U5P 501 C 1 HETATM 12 C C3' U5P . . . D 4 106.794 88.02 69.667 1 121.7 ? C3' U5P 501 C 1 HETATM 13 C C4' U5P . . . D 4 106.601 86.692 69.038 1 121.7 ? C4' U5P 501 C 1 HETATM 14 O O3' U5P . . . D 4 106.4 87.978 71.046 1 121.7 ? O3' U5P 501 C 1 HETATM 15 O O4' U5P . . . D 4 107.718 86.517 68.103 1 121.7 ? O4' U5P 501 C 1 HETATM 16 C C5' U5P . . . D 4 105.311 86.698 68.301 1 121.7 ? C5' U5P 501 C 1 HETATM 17 O O5' U5P . . . D 4 104.691 85.467 68.516 1 121.7 ? O5' U5P 501 C 1 HETATM 18 P P U5P . . . D 4 104.742 84.602 67.117 1 121.7 ? P U5P 501 C 1 HETATM 19 O O2P U5P . . . D 4 105.942 84.964 66.371 1 121.7 ? O2P U5P 501 C 1 HETATM 20 O O3P U5P . . . D 4 104.787 83.002 67.488 1 121.7 ? O3P U5P 501 C 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #