data_8RFE # _model_server_result.job_id zDjz7eLTMM4NM_CmIz_Jbw _model_server_result.datetime_utc '2024-12-26 10:26:58' _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 8rfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2902}' # _entry.id 8RFE # _exptl.entry_id 8RFE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _entity.pdbx_number_of_molecules 3 _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 8RFE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RFE _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 C N N ? 3 D N N ? 3 E 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 BGC BGC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O2 HO2 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O2 HO2 . sing 4 ? 2 5 4 BGC BGC C1 O1 . O2 HO2 . sing 5 ? 2 6 5 BGC BGC C1 O1 . O2 HO2 . sing 6 ? 2 7 6 BGC BGC C1 O1 . O2 HO2 . sing 7 ? 2 8 7 BGC BGC C1 O1 . O2 HO2 . sing 8 ? 2 9 8 BGC BGC C1 O1 . O2 HO2 . 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 B BGC 1 B 1 BGC B 3 BGC 2 n B BGC 2 B 2 BGC B 4 BGC 2 n B BGC 3 B 3 BGC B 5 BGC 2 n B BGC 4 B 4 BGC B 6 BGC 2 n B BGC 5 B 5 BGC B 7 BGC 2 n B BGC 6 B 6 BGC B 8 BGC 2 n B BGC 7 B 7 BGC B 9 BGC 2 n B BGC 8 B 8 BGC B 10 BGC 2 n B BGC 9 B 9 BGC B 11 BGC # 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 B O2 BGC . B BGC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 B O2 BGC . B BGC 2 1_555 B C1 BGC . B BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B O2 BGC . B BGC 3 1_555 B C1 BGC . B BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B O2 BGC . B BGC 4 1_555 B C1 BGC . B BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B O2 BGC . B BGC 5 1_555 B C1 BGC . B BGC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B O2 BGC . B BGC 6 1_555 B C1 BGC . B BGC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B O2 BGC . B BGC 7 1_555 B C1 BGC . B BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 B O2 BGC . B BGC 8 1_555 B C1 BGC . B BGC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 380 n n N1 C6 UPG sing 381 n n N1 C1C UPG sing 382 n n C2 N3 UPG sing 383 n n C2 O2 UPG doub 384 n n N3 C4 UPG sing 385 n n N3 HN3 UPG sing 386 n n C4 C5 UPG sing 387 n n C4 O4 UPG doub 388 n n C5 C6 UPG doub 389 n n C5 H5 UPG sing 390 n n C6 H6 UPG sing 391 n n C1C C2C UPG sing 392 n n C1C O4C UPG sing 393 n n C1C H1C UPG sing 394 n n C2C O2C UPG sing 395 n n C2C C3C UPG sing 396 n n C2C H2C UPG sing 397 n n O2C HO2C UPG sing 398 n n C3C C4C UPG sing 399 n n C3C O3C UPG sing 400 n n C3C H3C UPG sing 401 n n C4C O4C UPG sing 402 n n C4C C5C UPG sing 403 n n C4C H4C UPG sing 404 n n O3C HO3C UPG sing 405 n n C5C O5C UPG sing 406 n n C5C H5C1 UPG sing 407 n n C5C H5C2 UPG sing 408 n n O5C PA UPG sing 409 n n PA O1A UPG doub 410 n n PA O2A UPG sing 411 n n PA O3A UPG sing 412 n n O2A HOA2 UPG sing 413 n n O3A PB UPG sing 414 n n PB O1B UPG doub 415 n n PB O2B UPG sing 416 n n PB O3B UPG sing 417 n n O2B HOB2 UPG sing 418 n n O3B C1' UPG sing 419 n n C1' C2' UPG sing 420 n n C1' O5' UPG sing 421 n n C1' H1' UPG sing 422 n n C2' C3' UPG sing 423 n n C2' O2' UPG sing 424 n n C2' H2' UPG sing 425 n n C3' C4' UPG sing 426 n n C3' O3' UPG sing 427 n n C3' H3' UPG sing 428 n n C4' C5' UPG sing 429 n n C4' O4' UPG sing 430 n n C4' H4' UPG sing 431 n n C5' C6' UPG sing 432 n n C5' O5' UPG sing 433 n n C5' H5' UPG sing 434 n n C6' O6' UPG sing 435 n n C6' "H6'1" UPG sing 436 n n C6' "H6'2" UPG sing 437 n n O2' HO2' UPG sing 438 n n O3' HO3' UPG sing 439 n n O4' HO4' UPG sing 440 n n O6' HO6' UPG sing 441 n n # _atom_sites.entry_id 8RFE _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 C 3 UPG A 1 2901 2901 UPG UPG . D 3 UPG A 1 2902 2902 UPG UPG . E 3 UPG A 1 2903 2903 UPG UPG . # 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 . . . D 3 196.289 185.78 273.225 1 23.9 ? N1 UPG 2902 A 1 HETATM 2 C C2 UPG . . . D 3 196.315 185.571 271.858 1 23.29 ? C2 UPG 2902 A 1 HETATM 3 N N3 UPG . . . D 3 195.472 184.585 271.412 1 22.31 ? N3 UPG 2902 A 1 HETATM 4 C C4 UPG . . . D 3 194.624 183.807 272.174 1 24.34 ? C4 UPG 2902 A 1 HETATM 5 C C5 UPG . . . D 3 194.654 184.086 273.579 1 23.78 ? C5 UPG 2902 A 1 HETATM 6 C C6 UPG . . . D 3 195.467 185.045 274.045 1 22.9 ? C6 UPG 2902 A 1 HETATM 7 O O2 UPG . . . D 3 197.033 186.211 271.103 1 22.06 ? O2 UPG 2902 A 1 HETATM 8 O O4 UPG . . . D 3 193.926 182.957 271.623 1 22.33 ? O4 UPG 2902 A 1 HETATM 9 C C1C UPG . . . D 3 197.168 186.834 273.763 1 22.68 ? C1C UPG 2902 A 1 HETATM 10 C C2C UPG . . . D 3 196.457 188.182 273.874 1 25.7 ? C2C UPG 2902 A 1 HETATM 11 O O2C UPG . . . D 3 196.691 188.925 272.697 1 23.54 ? O2C UPG 2902 A 1 HETATM 12 C C3C UPG . . . D 3 197.148 188.793 275.096 1 25.06 ? C3C UPG 2902 A 1 HETATM 13 C C4C UPG . . . D 3 197.37 187.564 275.988 1 21.74 ? C4C UPG 2902 A 1 HETATM 14 O O4C UPG . . . D 3 197.572 186.463 275.064 1 23.46 ? O4C UPG 2902 A 1 HETATM 15 O O3C UPG . . . D 3 198.372 189.425 274.746 1 24.6 ? O3C UPG 2902 A 1 HETATM 16 C C5C UPG . . . D 3 196.254 187.229 276.946 1 26.48 ? C5C UPG 2902 A 1 HETATM 17 O O5C UPG . . . D 3 196.787 187.153 278.292 1 26.47 ? O5C UPG 2902 A 1 HETATM 18 P PA UPG . . . D 3 196.068 187.993 279.453 1 30.73 ? PA UPG 2902 A 1 HETATM 19 O O1A UPG . . . D 3 195.84 187.11 280.634 1 25.13 ? O1A UPG 2902 A 1 HETATM 20 O O2A UPG . . . D 3 194.9 188.723 278.881 1 33.07 ? O2A UPG 2902 A 1 HETATM 21 O O3A UPG . . . D 3 197.217 189.05 279.821 1 29.6 ? O3A UPG 2902 A 1 HETATM 22 P PB UPG . . . D 3 197.642 190.476 279.223 1 31.34 ? PB UPG 2902 A 1 HETATM 23 O O1B UPG . . . D 3 197.385 191.528 280.252 1 32.13 ? O1B UPG 2902 A 1 HETATM 24 O O2B UPG . . . D 3 197.022 190.661 277.88 1 33.54 ? O2B UPG 2902 A 1 HETATM 25 O O3B UPG . . . D 3 199.226 190.301 279.042 1 28.67 ? O3B UPG 2902 A 1 HETATM 26 C C1' UPG . . . D 3 199.808 189.274 278.284 1 28.03 ? C1' UPG 2902 A 1 HETATM 27 C C2' UPG . . . D 3 200.422 188.275 279.252 1 26.37 ? C2' UPG 2902 A 1 HETATM 28 C C3' UPG . . . D 3 201.036 187.121 278.49 1 27.25 ? C3' UPG 2902 A 1 HETATM 29 C C4' UPG . . . D 3 201.056 187.425 277.004 1 28.37 ? C4' UPG 2902 A 1 HETATM 30 C C5' UPG . . . D 3 201.623 188.817 276.768 1 27.96 ? C5' UPG 2902 A 1 HETATM 31 C C6' UPG . . . D 3 201.706 189.196 275.307 1 27.79 ? C6' UPG 2902 A 1 HETATM 32 O O2' UPG . . . D 3 201.377 188.925 280.086 1 25.44 ? O2' UPG 2902 A 1 HETATM 33 O O3' UPG . . . D 3 200.286 185.933 278.737 1 25.38 ? O3' UPG 2902 A 1 HETATM 34 O O4' UPG . . . D 3 201.872 186.471 276.332 1 29.95 ? O4' UPG 2902 A 1 HETATM 35 O O5' UPG . . . D 3 200.797 189.808 277.42 1 31.91 ? O5' UPG 2902 A 1 HETATM 36 O O6' UPG . . . D 3 200.971 188.294 274.481 1 23.12 ? O6' UPG 2902 A 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #