data_8HJN # _model_server_result.job_id jTKDucEMxttquMZYg2369A _model_server_result.datetime_utc '2025-02-17 18:17:30' _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 8hjn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 8HJN # _exptl.entry_id 8HJN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 8HJN _cell.length_a 64.22 _cell.length_b 80.095 _cell.length_c 172.508 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HJN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 1 1 B,D 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 ? 2 C N N ? 2 D 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 disulf ? disulf1 A SG CYS 199 A CYS 199 1_555 A SG CYS 204 A CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 B SG CYS 199 B CYS 199 1_555 B SG CYS 204 B CYS 204 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 8HJN _atom_sites.fract_transf_matrix[1][1] 0.015571 _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] 0.012485 _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] 0.005797 _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 UPG A 1 501 2 UPG UPG . D 2 UPG B 1 501 1 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 . . . C 2 12.56 -13.874 -21.486 1 35 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . C 2 13.896 -13.903 -21.131 1 48.94 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . C 2 14.266 -12.964 -20.202 1 54.09 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . C 2 13.451 -12.03 -19.593 1 50.36 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . C 2 12.078 -12.071 -20.006 1 42.98 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . C 2 11.688 -12.976 -20.916 1 42.36 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . C 2 14.695 -14.691 -21.62 1 54.51 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . C 2 13.934 -11.254 -18.768 1 49.68 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . C 2 12.108 -14.864 -22.482 1 37.57 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . C 2 11.425 -16.083 -21.862 1 45.14 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . C 2 12.406 -17.033 -21.502 1 37.38 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . C 2 10.53 -16.509 -23.031 1 48.05 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . C 2 10.019 -15.141 -23.503 1 51.31 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . C 2 11.159 -14.258 -23.334 1 56.56 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . C 2 11.318 -17.124 -24.041 1 43.6 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . C 2 8.858 -14.572 -22.728 1 41.3 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . C 2 7.798 -15.554 -22.668 1 57.95 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . C 2 6.324 -14.985 -22.408 1 71.25 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . C 2 6.346 -14.098 -21.208 1 60.72 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . C 2 5.335 -16.101 -22.473 1 58.18 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . C 2 6.162 -14.067 -23.713 1 82.89 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . C 2 5.83 -12.512 -23.92 1 105.03 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . C 2 5.916 -12.192 -25.377 1 74.46 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . C 2 6.644 -11.702 -22.965 1 86.68 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . C 2 4.291 -12.494 -23.459 1 91.5 ? O3B UPG 501 A 1 HETATM 26 C C1' UPG . . . C 2 3.287 -13.049 -24.268 1 93.44 ? C1' UPG 501 A 1 HETATM 27 C C2' UPG . . . C 2 1.923 -12.535 -23.826 1 87.33 ? C2' UPG 501 A 1 HETATM 28 C C3' UPG . . . C 2 0.877 -12.971 -24.836 1 75.53 ? C3' UPG 501 A 1 HETATM 29 C C4' UPG . . . C 2 1.437 -14.052 -25.757 1 76.39 ? C4' UPG 501 A 1 HETATM 30 C C5' UPG . . . C 2 2.241 -15.099 -24.968 1 72.86 ? C5' UPG 501 A 1 HETATM 31 C C6' UPG . . . C 2 2.885 -16.154 -25.841 1 70.02 ? C6' UPG 501 A 1 HETATM 32 O O2' UPG . . . C 2 1.6 -13.07 -22.545 1 86.25 ? O2' UPG 501 A 1 HETATM 33 O O3' UPG . . . C 2 0.472 -11.843 -25.612 1 79.55 ? O3' UPG 501 A 1 HETATM 34 O O4' UPG . . . C 2 0.387 -14.686 -26.484 1 90.49 ? O4' UPG 501 A 1 HETATM 35 O O5' UPG . . . C 2 3.309 -14.466 -24.221 1 78.14 ? O5' UPG 501 A 1 HETATM 36 O O6' UPG . . . C 2 3.933 -15.617 -26.652 1 56.7 ? O6' UPG 501 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #