data_7X05 # _model_server_result.job_id IjtjTFymcVx8lV1IOAjYog _model_server_result.datetime_utc '2025-07-01 03:13:10' _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 7x05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 7X05 # _exptl.entry_id 7X05 _exptl.method 'ELECTRON MICROSCOPY' # _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 7X05 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7X05 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 ? 3 E N N ? 3 G N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 997 NAG 2 n C NAG 2 C 2 NAG A 998 NAG 2 n C NAG 3 C 3 NAG A 999 NAG 2 n D NAG 1 D 1 NAG B 997 NAG 2 n D NAG 2 D 2 NAG B 998 NAG 2 n D NAG 3 D 3 NAG B 999 NAG # 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 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 C O4 NAG . C NAG 2 1_555 C C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 D O4 NAG . D NAG 2 1_555 D C1 NAG . D NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 E PB UDP . A UDP 1001 1_555 F MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 E O1B UDP . A UDP 1001 1_555 F MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 E O2B UDP . A UDP 1001 1_555 F MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 E O3B UDP . A UDP 1001 1_555 F MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 G PB UDP . B UDP 1001 1_555 H MN MN . B MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc6 G O1B UDP . B UDP 1001 1_555 H MN MN . B MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 G O2B UDP . B UDP 1001 1_555 H MN MN . B MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 G O3B UDP . B UDP 1001 1_555 H MN MN . B MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 ? # 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 UDP sing 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 7X05 _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 E 3 UDP A 1 1001 921 UDP UDP . F 4 MN A 1 1002 922 MN MN . G 3 UDP B 1 1001 921 UDP UDP . H 4 MN B 1 1002 922 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 . . . E 3 17.463 10.664 21.05 1 38.81 ? N1 UDP 1001 A 1 HETATM 2 C C2 UDP . . . E 3 16.795 11.12 22.169 1 38.81 ? C2 UDP 1001 A 1 HETATM 3 N N3 UDP . . . E 3 15.672 10.408 22.504 1 38.81 ? N3 UDP 1001 A 1 HETATM 4 C C4 UDP . . . E 3 15.16 9.308 21.844 1 38.81 ? C4 UDP 1001 A 1 HETATM 5 C C5 UDP . . . E 3 15.909 8.896 20.698 1 38.81 ? C5 UDP 1001 A 1 HETATM 6 C C6 UDP . . . E 3 17.014 9.573 20.342 1 38.81 ? C6 UDP 1001 A 1 HETATM 7 O O2 UDP . . . E 3 17.169 12.085 22.82 1 38.81 ? O2 UDP 1001 A 1 HETATM 8 O O4 UDP . . . E 3 14.129 8.764 22.267 1 38.81 ? O4 UDP 1001 A 1 HETATM 9 C C1' UDP . . . E 3 18.677 11.382 20.641 1 38.81 ? C1' UDP 1001 A 1 HETATM 10 C C2' UDP . . . E 3 19.883 10.462 20.439 1 38.81 ? C2' UDP 1001 A 1 HETATM 11 O O2' UDP . . . E 3 20.642 10.353 21.638 1 38.81 ? O2' UDP 1001 A 1 HETATM 12 C C3' UDP . . . E 3 20.638 11.203 19.338 1 38.81 ? C3' UDP 1001 A 1 HETATM 13 C C4' UDP . . . E 3 19.5 11.721 18.469 1 38.81 ? C4' UDP 1001 A 1 HETATM 14 O O4' UDP . . . E 3 18.425 12.005 19.391 1 38.81 ? O4' UDP 1001 A 1 HETATM 15 O O3' UDP . . . E 3 21.408 12.282 19.852 1 38.81 ? O3' UDP 1001 A 1 HETATM 16 C C5' UDP . . . E 3 19.019 10.762 17.41 1 38.81 ? C5' UDP 1001 A 1 HETATM 17 O O5' UDP . . . E 3 19.917 10.83 16.282 1 38.81 ? O5' UDP 1001 A 1 HETATM 18 P PA UDP . . . E 3 19.817 9.8 15.087 1 38.81 ? PA UDP 1001 A 1 HETATM 19 O O1A UDP . . . E 3 18.773 10.244 14.066 1 38.81 ? O1A UDP 1001 A 1 HETATM 20 O O2A UDP . . . E 3 19.643 8.457 15.687 1 38.81 ? O2A UDP 1001 A 1 HETATM 21 O O3A UDP . . . E 3 21.223 9.897 14.355 1 38.81 ? O3A UDP 1001 A 1 HETATM 22 P PB UDP . . . E 3 22.622 9.586 15.032 1 38.81 ? PB UDP 1001 A 1 HETATM 23 O O1B UDP . . . E 3 23.368 8.512 14.313 1 38.81 ? O1B UDP 1001 A 1 HETATM 24 O O2B UDP . . . E 3 22.24 9.211 16.455 1 38.81 ? O2B UDP 1001 A 1 HETATM 25 O O3B UDP . . . E 3 23.32 10.948 15.023 1 38.81 ? O3B UDP 1001 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #