data_6L8Z # _model_server_result.job_id HYTvlXjkFJWeZTlNsfqNgg _model_server_result.datetime_utc '2024-11-24 20:21:17' _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 6l8z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6L8Z # _exptl.entry_id 6L8Z _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 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 6L8Z _cell.length_a 49.311 _cell.length_b 69.153 _cell.length_c 141.148 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L8Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 259 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 259 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 331 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 331 _struct_conn.ptnr2_symmetry 1_555 _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 2.041 _struct_conn.pdbx_value_order ? # _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 358 n n N1 C6 UPG sing 359 n n N1 C1C UPG sing 360 n n C2 N3 UPG sing 361 n n C2 O2 UPG doub 362 n n N3 C4 UPG sing 363 n n N3 HN3 UPG sing 364 n n C4 C5 UPG sing 365 n n C4 O4 UPG doub 366 n n C5 C6 UPG doub 367 n n C5 H5 UPG sing 368 n n C6 H6 UPG sing 369 n n C1C C2C UPG sing 370 n n C1C O4C UPG sing 371 n n C1C H1C UPG sing 372 n n C2C O2C UPG sing 373 n n C2C C3C UPG sing 374 n n C2C H2C UPG sing 375 n n O2C HO2C UPG sing 376 n n C3C C4C UPG sing 377 n n C3C O3C UPG sing 378 n n C3C H3C UPG sing 379 n n C4C O4C UPG sing 380 n n C4C C5C UPG sing 381 n n C4C H4C UPG sing 382 n n O3C HO3C UPG sing 383 n n C5C O5C UPG sing 384 n n C5C H5C1 UPG sing 385 n n C5C H5C2 UPG sing 386 n n O5C PA UPG sing 387 n n PA O1A UPG doub 388 n n PA O2A UPG sing 389 n n PA O3A UPG sing 390 n n O2A HOA2 UPG sing 391 n n O3A PB UPG sing 392 n n PB O1B UPG doub 393 n n PB O2B UPG sing 394 n n PB O3B UPG sing 395 n n O2B HOB2 UPG sing 396 n n O3B C1' UPG sing 397 n n C1' C2' UPG sing 398 n n C1' O5' UPG sing 399 n n C1' H1' UPG sing 400 n n C2' C3' UPG sing 401 n n C2' O2' UPG sing 402 n n C2' H2' UPG sing 403 n n C3' C4' UPG sing 404 n n C3' O3' UPG sing 405 n n C3' H3' UPG sing 406 n n C4' C5' UPG sing 407 n n C4' O4' UPG sing 408 n n C4' H4' UPG sing 409 n n C5' C6' UPG sing 410 n n C5' O5' UPG sing 411 n n C5' H5' UPG sing 412 n n C6' O6' UPG sing 413 n n C6' "H6'1" UPG sing 414 n n C6' "H6'2" UPG sing 415 n n O2' HO2' UPG sing 416 n n O3' HO3' UPG sing 417 n n O4' HO4' UPG sing 418 n n O6' HO6' UPG sing 419 n n # _atom_sites.entry_id 6L8Z _atom_sites.fract_transf_matrix[1][1] 0.020279 _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] 0.014461 _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] 0.007085 _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 UPG A 1 501 501 UPG UPG . C 3 HOH A 1 601 64 HOH HOH . C 3 HOH A 2 602 39 HOH HOH . C 3 HOH A 3 603 24 HOH HOH . C 3 HOH A 4 604 18 HOH HOH . C 3 HOH A 5 605 16 HOH HOH . C 3 HOH A 6 606 29 HOH HOH . C 3 HOH A 7 607 51 HOH HOH . C 3 HOH A 8 608 6 HOH HOH . C 3 HOH A 9 609 35 HOH HOH . C 3 HOH A 10 610 22 HOH HOH . C 3 HOH A 11 611 27 HOH HOH . C 3 HOH A 12 612 38 HOH HOH . C 3 HOH A 13 613 34 HOH HOH . C 3 HOH A 14 614 12 HOH HOH . C 3 HOH A 15 615 3 HOH HOH . C 3 HOH A 16 616 103 HOH HOH . C 3 HOH A 17 617 62 HOH HOH . C 3 HOH A 18 618 32 HOH HOH . C 3 HOH A 19 619 56 HOH HOH . C 3 HOH A 20 620 1 HOH HOH . C 3 HOH A 21 621 8 HOH HOH . C 3 HOH A 22 622 31 HOH HOH . C 3 HOH A 23 623 40 HOH HOH . C 3 HOH A 24 624 41 HOH HOH . C 3 HOH A 25 625 101 HOH HOH . C 3 HOH A 26 626 84 HOH HOH . C 3 HOH A 27 627 36 HOH HOH . C 3 HOH A 28 628 28 HOH HOH . C 3 HOH A 29 629 11 HOH HOH . C 3 HOH A 30 630 4 HOH HOH . C 3 HOH A 31 631 19 HOH HOH . C 3 HOH A 32 632 20 HOH HOH . C 3 HOH A 33 633 15 HOH HOH . C 3 HOH A 34 634 9 HOH HOH . C 3 HOH A 35 635 10 HOH HOH . C 3 HOH A 36 636 14 HOH HOH . C 3 HOH A 37 637 37 HOH HOH . C 3 HOH A 38 638 69 HOH HOH . C 3 HOH A 39 639 70 HOH HOH . C 3 HOH A 40 640 5 HOH HOH . C 3 HOH A 41 641 13 HOH HOH . C 3 HOH A 42 642 77 HOH HOH . C 3 HOH A 43 643 82 HOH HOH . C 3 HOH A 44 644 26 HOH HOH . C 3 HOH A 45 645 58 HOH HOH . C 3 HOH A 46 646 17 HOH HOH . C 3 HOH A 47 647 23 HOH HOH . C 3 HOH A 48 648 67 HOH HOH . C 3 HOH A 49 649 30 HOH HOH . C 3 HOH A 50 650 88 HOH HOH . C 3 HOH A 51 651 93 HOH HOH . C 3 HOH A 52 652 87 HOH HOH . C 3 HOH A 53 653 44 HOH HOH . C 3 HOH A 54 654 47 HOH HOH . C 3 HOH A 55 655 110 HOH HOH . C 3 HOH A 56 656 95 HOH HOH . C 3 HOH A 57 657 90 HOH HOH . # 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 . . . B 2 36.172 23.213 9.218 1 66.63 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . B 2 36.272 23.478 7.865 1 66.86 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . B 2 35.334 24.346 7.383 1 75.18 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . B 2 34.339 24.974 8.098 1 71.52 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . B 2 34.296 24.642 9.487 1 63.71 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . B 2 35.193 23.784 9.985 1 65.78 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . B 2 37.116 22.984 7.142 1 57.57 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . B 2 33.58 25.743 7.518 1 78.54 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . B 2 37.123 22.257 9.8 1 71.66 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . B 2 38.038 22.889 10.837 1 66.45 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . B 2 39.183 23.17 10.076 1 61.08 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . B 2 38.261 21.744 11.828 1 72.27 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . B 2 36.977 20.912 11.727 1 71.2 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . B 2 36.398 21.234 10.44 1 72.73 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . B 2 39.402 20.957 11.526 1 74.83 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . B 2 35.958 21.165 12.806 1 72.76 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . B 2 35.884 22.584 13.025 1 78.03 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . B 2 34.865 23.188 14.083 1 84.26 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . B 2 33.824 22.192 14.431 1 71.88 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . B 2 34.397 24.504 13.588 1 72.43 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . B 2 35.855 23.398 15.327 1 78.66 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . B 2 36.738 22.52 16.324 1 64.63 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . B 2 37.842 23.328 16.857 1 58.38 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . B 2 37.002 21.181 15.76 1 72.65 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . B 2 35.726 22.31 17.497 1 77.5 ? O3B UPG 501 A 1 HETATM 26 C C1' UPG . . . B 2 35.217 21.047 17.689 1 82.17 ? C1' UPG 501 A 1 HETATM 27 C C2' UPG . . . B 2 33.763 21.268 17.933 1 92.29 ? C2' UPG 501 A 1 HETATM 28 C C3' UPG . . . B 2 33.574 22.085 19.17 1 87.17 ? C3' UPG 501 A 1 HETATM 29 C C4' UPG . . . B 2 34.36 21.497 20.331 1 81.22 ? C4' UPG 501 A 1 HETATM 30 C C5' UPG . . . B 2 35.794 21.33 19.934 1 79.75 ? C5' UPG 501 A 1 HETATM 31 C C6' UPG . . . B 2 36.661 20.751 21.013 1 74.29 ? C6' UPG 501 A 1 HETATM 32 O O2' UPG . . . B 2 33.206 21.971 16.824 1 96.78 ? O2' UPG 501 A 1 HETATM 33 O O3' UPG . . . B 2 32.17 22.08 19.418 1 102.33 ? O3' UPG 501 A 1 HETATM 34 O O4' UPG . . . B 2 34.358 22.349 21.453 1 66.84 ? O4' UPG 501 A 1 HETATM 35 O O5' UPG . . . B 2 35.842 20.462 18.809 1 78.95 ? O5' UPG 501 A 1 HETATM 36 O O6' UPG . . . B 2 37.345 21.782 21.663 1 52.46 ? O6' UPG 501 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #