data_5H60 # _model_server_result.job_id yH2t7RqWf0fkhKKYooRn4A _model_server_result.datetime_utc '2024-10-20 00:41:11' _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 5h60 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5H60 # _exptl.entry_id 5H60 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 5H60 _cell.length_a 115.94 _cell.length_b 115.94 _cell.length_c 100.08 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H60 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _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 _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 2 _struct_asym.id B _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 OD2 ASP 225 A ASP 225 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? metalc ? metalc2 A OD1 ASN 322 A ASN 322 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc3 A OG SER 324 A SER 324 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? covale ? covale1 A NE2 GLN 328 A GLN 328 1_555 A C ARG 333 A ARG 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale2 A NE2 GLN 328 A GLN 328 1_555 A O ARG 333 A ARG 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? metalc ? metalc4 B O1A UDP . A UDP 401 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 B O3B UDP . A UDP 401 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? # _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 5H60 _atom_sites.fract_transf_matrix[1][1] 0.008625 _atom_sites.fract_transf_matrix[1][2] 0.00498 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009959 _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] 0.009992 _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 UDP A 1 401 1 UDP UDP . C 3 MN A 1 402 1 MN MN . # 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 . . . B 2 14.085 41.747 23.233 1 85.02 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 12.91 41.708 24.01 1 89.31 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 12.988 41.427 25.33 1 92.88 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 14.175 41.202 25.927 1 95.85 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 15.338 41.248 25.173 1 93.79 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 15.27 41.555 23.815 1 88.05 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 11.798 41.932 23.475 1 92.87 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 14.269 40.943 27.145 1 97.7 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 13.998 42.057 21.795 1 82.73 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 13.946 43.548 21.622 1 84.37 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 12.877 43.88 20.746 1 89.77 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 15.262 43.947 21.006 1 84.05 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 15.91 42.645 20.587 1 82.27 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 15.125 41.57 21.1 1 77.36 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 15.046 44.799 19.889 1 85.58 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 17.316 42.582 21.144 1 84.99 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 17.757 41.256 21.351 1 94.91 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 19.361 41.049 21.199 1 91.96 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 19.677 41.192 19.749 1 95.01 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 20.059 41.988 22.13 1 81.67 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 19.71 39.508 21.554 1 105.25 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 20.482 38.555 20.49 1 107.41 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 19.524 38.203 19.382 1 110.64 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 20.826 37.289 21.256 1 119.23 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 21.722 39.288 20.015 1 101.45 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 25 #