data_9J0B # _model_server_result.job_id xw24COoxn7kMWW6_lqKn3w _model_server_result.datetime_utc '2025-07-03 14:41:04' _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 9j0b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 9J0B # _exptl.entry_id 9J0B _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 566.302 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 90 _cell.entry_id 9J0B _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J0B _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 disulf ? disulf1 D SG CYS 257 R CYS 94 1_555 D SG CYS 335 R CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 E SG CYS 60 S CYS 22 1_555 E SG CYS 134 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 UPG sing 356 n n N1 C6 UPG sing 357 n n N1 C1C UPG sing 358 n n C2 N3 UPG sing 359 n n C2 O2 UPG doub 360 n n N3 C4 UPG sing 361 n n N3 HN3 UPG sing 362 n n C4 C5 UPG sing 363 n n C4 O4 UPG doub 364 n n C5 C6 UPG doub 365 n n C5 H5 UPG sing 366 n n C6 H6 UPG sing 367 n n C1C C2C UPG sing 368 n n C1C O4C UPG sing 369 n n C1C H1C UPG sing 370 n n C2C O2C UPG sing 371 n n C2C C3C UPG sing 372 n n C2C H2C UPG sing 373 n n O2C HO2C UPG sing 374 n n C3C C4C UPG sing 375 n n C3C O3C UPG sing 376 n n C3C H3C UPG sing 377 n n C4C O4C UPG sing 378 n n C4C C5C UPG sing 379 n n C4C H4C UPG sing 380 n n O3C HO3C UPG sing 381 n n C5C O5C UPG sing 382 n n C5C H5C1 UPG sing 383 n n C5C H5C2 UPG sing 384 n n O5C PA UPG sing 385 n n PA O1A UPG doub 386 n n PA O2A UPG sing 387 n n PA O3A UPG sing 388 n n O2A HOA2 UPG sing 389 n n O3A PB UPG sing 390 n n PB O1B UPG doub 391 n n PB O2B UPG sing 392 n n PB O3B UPG sing 393 n n O2B HOB2 UPG sing 394 n n O3B C1' UPG sing 395 n n C1' C2' UPG sing 396 n n C1' O5' UPG sing 397 n n C1' H1' UPG sing 398 n n C2' C3' UPG sing 399 n n C2' O2' UPG sing 400 n n C2' H2' UPG sing 401 n n C3' C4' UPG sing 402 n n C3' O3' UPG sing 403 n n C3' H3' UPG sing 404 n n C4' C5' UPG sing 405 n n C4' O4' UPG sing 406 n n C4' H4' UPG sing 407 n n C5' C6' UPG sing 408 n n C5' O5' UPG sing 409 n n C5' H5' UPG sing 410 n n C6' O6' UPG sing 411 n n C6' "H6'1" UPG sing 412 n n C6' "H6'2" UPG sing 413 n n O2' HO2' UPG sing 414 n n O3' HO3' UPG sing 415 n n O4' HO4' UPG sing 416 n n O6' HO6' UPG sing 417 n n # _atom_sites.entry_id 9J0B _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 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id UPG _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id UPG _pdbx_nonpoly_scheme.auth_mon_id UPG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 UPG . . . F 6 130.119 142.881 101.794 1 39.59 ? N1 UPG 401 R 1 HETATM 2 C C2 UPG . . . F 6 130.627 142.755 103.102 1 40.23 ? C2 UPG 401 R 1 HETATM 3 N N3 UPG . . . F 6 131.657 141.939 103.351 1 42.51 ? N3 UPG 401 R 1 HETATM 4 C C4 UPG . . . F 6 132.221 141.232 102.366 1 50.52 ? C4 UPG 401 R 1 HETATM 5 C C5 UPG . . . F 6 131.741 141.338 101.067 1 48.14 ? C5 UPG 401 R 1 HETATM 6 C C6 UPG . . . F 6 130.673 142.183 100.798 1 42.91 ? C6 UPG 401 R 1 HETATM 7 O O2 UPG . . . F 6 130.111 143.409 104.034 1 43.89 ? O2 UPG 401 R 1 HETATM 8 O O4 UPG . . . F 6 133.183 140.474 102.614 1 46.43 ? O4 UPG 401 R 1 HETATM 9 C C1C UPG . . . F 6 128.991 143.776 101.527 1 40.05 ? C1C UPG 401 R 1 HETATM 10 C C2C UPG . . . F 6 129.049 144.307 100.104 1 42.29 ? C2C UPG 401 R 1 HETATM 11 O O2C UPG . . . F 6 129.316 145.712 100.102 1 42.89 ? O2C UPG 401 R 1 HETATM 12 C C3C UPG . . . F 6 127.684 144.038 99.507 1 47.52 ? C3C UPG 401 R 1 HETATM 13 C C4C UPG . . . F 6 126.994 143.092 100.473 1 40.36 ? C4C UPG 401 R 1 HETATM 14 O O4C UPG . . . F 6 127.78 143.03 101.664 1 41.51 ? O4C UPG 401 R 1 HETATM 15 O O3C UPG . . . F 6 126.944 145.257 99.409 1 44.48 ? O3C UPG 401 R 1 HETATM 16 C C5C UPG . . . F 6 126.887 141.688 99.896 1 40.98 ? C5C UPG 401 R 1 HETATM 17 O O5C UPG . . . F 6 127.186 141.697 98.503 1 46.67 ? O5C UPG 401 R 1 HETATM 18 P PA UPG . . . F 6 128.23 140.635 97.888 1 54.01 ? PA UPG 401 R 1 HETATM 19 O O1A UPG . . . F 6 128.928 141.261 96.705 1 43.31 ? O1A UPG 401 R 1 HETATM 20 O O2A UPG . . . F 6 129.046 140.069 99.025 1 51.74 ? O2A UPG 401 R 1 HETATM 21 O O3A UPG . . . F 6 127.237 139.479 97.378 1 42.07 ? O3A UPG 401 R 1 HETATM 22 P PB UPG . . . F 6 126.391 139.585 96.015 1 49.57 ? PB UPG 401 R 1 HETATM 23 O O1B UPG . . . F 6 126.703 138.384 95.159 1 49.31 ? O1B UPG 401 R 1 HETATM 24 O O2B UPG . . . F 6 126.515 140.985 95.457 1 38.3 ? O2B UPG 401 R 1 HETATM 25 O O3B UPG . . . F 6 124.932 139.371 96.664 1 50.09 ? O3B UPG 401 R 1 HETATM 26 C C1' UPG . . . F 6 123.753 140.028 96.216 1 45.26 ? C1' UPG 401 R 1 HETATM 27 C C2' UPG . . . F 6 122.805 140.134 97.404 1 44.56 ? C2' UPG 401 R 1 HETATM 28 C C3' UPG . . . F 6 122.435 138.748 97.914 1 43.57 ? C3' UPG 401 R 1 HETATM 29 C C4' UPG . . . F 6 121.929 137.876 96.773 1 47.58 ? C4' UPG 401 R 1 HETATM 30 C C5' UPG . . . F 6 122.916 137.899 95.613 1 49.95 ? C5' UPG 401 R 1 HETATM 31 C C6' UPG . . . F 6 122.403 137.081 94.435 1 50.21 ? C6' UPG 401 R 1 HETATM 32 O O2' UPG . . . F 6 123.441 140.857 98.461 1 53.71 ? O2' UPG 401 R 1 HETATM 33 O O3' UPG . . . F 6 121.421 138.858 98.918 1 48.19 ? O3' UPG 401 R 1 HETATM 34 O O4' UPG . . . F 6 121.773 136.532 97.24 1 46.98 ? O4' UPG 401 R 1 HETATM 35 O O5' UPG . . . F 6 123.139 139.245 95.195 1 44.17 ? O5' UPG 401 R 1 HETATM 36 O O6' UPG . . . F 6 123.385 137.092 93.394 1 52.38 ? O6' UPG 401 R 1 # _model_server_stats.io_time_ms 1651 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #