data_5U6M # _model_server_result.job_id qRtHSZKOhDcw9ef7Zg8jAg _model_server_result.datetime_utc '2024-10-18 18:20:16' _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 5u6m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5U6M # _exptl.entry_id 5U6M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 90 _cell.entry_id 5U6M _cell.length_a 65.694 _cell.length_b 87.681 _cell.length_c 164.25 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U6M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G 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 A OH TYR 177 A TYR 177 1_555 C C1 BGC . A BGC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale2 B OH TYR 177 B TYR 177 1_555 F C1 BGC . B BGC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5U6M _atom_sites.fract_transf_matrix[1][1] 0.015222 _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] 0.011405 _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] 0.006088 _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 BGC A 1 501 501 BGC BGC . D 3 UDP A 1 502 2 UDP UDP . E 4 SAL A 1 503 3 SAL SAL . F 2 BGC B 1 501 501 BGC BGC . G 3 UDP B 1 502 1 UDP UDP . H 4 SAL B 1 503 4 SAL SAL . I 5 HOH A 1 601 3 HOH HOH . I 5 HOH A 2 602 1 HOH HOH . I 5 HOH A 3 603 4 HOH HOH . J 5 HOH B 1 601 5 HOH HOH . J 5 HOH B 2 602 2 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 N N1 UDP . . . D 3 70.044 71.476 41.815 1 55.44 ? N1 UDP 502 A 1 HETATM 2 C C2 UDP . . . D 3 70.648 72.546 42.568 1 58.15 ? C2 UDP 502 A 1 HETATM 3 N N3 UDP . . . D 3 72.047 72.409 42.959 1 55.58 ? N3 UDP 502 A 1 HETATM 4 C C4 UDP . . . D 3 72.83 71.249 42.599 1 59.11 ? C4 UDP 502 A 1 HETATM 5 C C5 UDP . . . D 3 72.2 70.146 41.834 1 47.57 ? C5 UDP 502 A 1 HETATM 6 C C6 UDP . . . D 3 70.773 70.286 41.451 1 48.58 ? C6 UDP 502 A 1 HETATM 7 O O2 UDP . . . D 3 70.002 73.48 42.836 1 62.37 ? O2 UDP 502 A 1 HETATM 8 O O4 UDP . . . D 3 73.968 71.18 42.932 1 65.97 ? O4 UDP 502 A 1 HETATM 9 C C1' UDP . . . D 3 68.648 71.627 41.463 1 59.45 ? C1' UDP 502 A 1 HETATM 10 C C2' UDP . . . D 3 68.389 71.642 39.93 1 55.82 ? C2' UDP 502 A 1 HETATM 11 O O2' UDP . . . D 3 68.355 72.95 39.535 1 55.96 ? O2' UDP 502 A 1 HETATM 12 C C3' UDP . . . D 3 67.058 70.95 39.862 1 55.04 ? C3' UDP 502 A 1 HETATM 13 C C4' UDP . . . D 3 66.989 70.073 40.911 1 57.28 ? C4' UDP 502 A 1 HETATM 14 O O4' UDP . . . D 3 68.085 70.539 41.94 1 57.58 ? O4' UDP 502 A 1 HETATM 15 O O3' UDP . . . D 3 66.045 72.021 40.004 1 52.64 ? O3' UDP 502 A 1 HETATM 16 C C5' UDP . . . D 3 67.39 68.678 40.573 1 63.26 ? C5' UDP 502 A 1 HETATM 17 O O5' UDP . . . D 3 66.216 68.008 40.12 1 75.54 ? O5' UDP 502 A 1 HETATM 18 P PA UDP . . . D 3 66.257 67.163 38.707 1 65.5 ? PA UDP 502 A 1 HETATM 19 O O1A UDP . . . D 3 67.342 67.726 37.858 1 64.75 ? O1A UDP 502 A 1 HETATM 20 O O2A UDP . . . D 3 64.902 67.018 38.078 1 57.28 ? O2A UDP 502 A 1 HETATM 21 O O3A UDP . . . D 3 66.818 65.664 39.1 1 73.28 ? O3A UDP 502 A 1 HETATM 22 P PB UDP . . . D 3 66.575 64.716 40.424 1 58.19 ? PB UDP 502 A 1 HETATM 23 O O1B UDP . . . D 3 67.191 63.343 40.303 1 68.51 ? O1B UDP 502 A 1 HETATM 24 O O2B UDP . . . D 3 65.094 64.688 40.597 1 55.96 ? O2B UDP 502 A 1 HETATM 25 O O3B UDP . . . D 3 67.32 65.62 41.356 1 66.89 ? O3B UDP 502 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #