data_5U6M # _model_server_result.job_id WrjVGYUCtQb8O3o7cw51bw _model_server_result.datetime_utc '2024-10-18 18:22:10' _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":"G","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 . . . G 3 43.593 87.244 74.292 1 74.52 ? N1 UDP 502 B 1 HETATM 2 C C2 UDP . . . G 3 43.221 87.803 73.013 1 70.88 ? C2 UDP 502 B 1 HETATM 3 N N3 UDP . . . G 3 41.809 87.821 72.658 1 70.93 ? N3 UDP 502 B 1 HETATM 4 C C4 UDP . . . G 3 40.779 87.286 73.527 1 70.71 ? C4 UDP 502 B 1 HETATM 5 C C5 UDP . . . G 3 41.165 86.702 74.838 1 71.4 ? C5 UDP 502 B 1 HETATM 6 C C6 UDP . . . G 3 42.612 86.688 75.212 1 73.17 ? C6 UDP 502 B 1 HETATM 7 O O2 UDP . . . G 3 44.052 88.238 72.319 1 72.08 ? O2 UDP 502 B 1 HETATM 8 O O4 UDP . . . G 3 39.643 87.319 73.179 1 68.7 ? O4 UDP 502 B 1 HETATM 9 C C1' UDP . . . G 3 45.012 87.247 74.583 1 68.52 ? C1' UDP 502 B 1 HETATM 10 C C2' UDP . . . G 3 45.452 88.134 75.789 1 71.23 ? C2' UDP 502 B 1 HETATM 11 O O2' UDP . . . G 3 45.83 89.357 75.278 1 72.17 ? O2' UDP 502 B 1 HETATM 12 C C3' UDP . . . G 3 46.557 87.251 76.352 1 73.38 ? C3' UDP 502 B 1 HETATM 13 C C4' UDP . . . G 3 46.287 85.937 76.052 1 63.6 ? C4' UDP 502 B 1 HETATM 14 O O4' UDP . . . G 3 45.243 85.978 74.874 1 66 ? O4' UDP 502 B 1 HETATM 15 O O3' UDP . . . G 3 47.85 87.559 75.701 1 70.31 ? O3' UDP 502 B 1 HETATM 16 C C5' UDP . . . G 3 45.652 85.19 77.173 1 50.86 ? C5' UDP 502 B 1 HETATM 17 O O5' UDP . . . G 3 46.736 84.756 77.999 1 61.13 ? O5' UDP 502 B 1 HETATM 18 P PA UDP . . . G 3 46.599 84.84 79.637 1 65.99 ? PA UDP 502 B 1 HETATM 19 O O1A UDP . . . G 3 46.047 86.192 80.005 1 68.51 ? O1A UDP 502 B 1 HETATM 20 O O2A UDP . . . G 3 47.913 84.537 80.296 1 71.3 ? O2A UDP 502 B 1 HETATM 21 O O3A UDP . . . G 3 45.441 83.755 80.089 1 57.29 ? O3A UDP 502 B 1 HETATM 22 P PB UDP . . . G 3 45.234 82.132 79.847 1 63.58 ? PB UDP 502 B 1 HETATM 23 O O1B UDP . . . G 3 44.568 82.137 78.494 1 58.36 ? O1B UDP 502 B 1 HETATM 24 O O2B UDP . . . G 3 44.344 81.492 80.912 1 68.32 ? O2B UDP 502 B 1 HETATM 25 O O3B UDP . . . G 3 46.649 81.588 79.825 1 54.34 ? O3B UDP 502 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #