data_5JSX # _model_server_result.job_id gLRXA4fZbP0WFKFOAUE9eQ _model_server_result.datetime_utc '2024-10-19 04:41:26' _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 5jsx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5JSX # _exptl.entry_id 5JSX _exptl.method 'X-RAY DIFFRACTION' # _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 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 5JSX _cell.length_a 98.78 _cell.length_b 98.78 _cell.length_c 127.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JSX _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc3 B MN MN . A MN 401 1_555 C O2B UPG . A UPG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 B MN MN . A MN 401 1_555 C O1A UPG . A UPG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 B MN MN . A MN 401 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc6 B MN MN . A MN 401 1_555 E O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 371 n n N1 C6 UPG sing 372 n n N1 C1C UPG sing 373 n n C2 N3 UPG sing 374 n n C2 O2 UPG doub 375 n n N3 C4 UPG sing 376 n n N3 HN3 UPG sing 377 n n C4 C5 UPG sing 378 n n C4 O4 UPG doub 379 n n C5 C6 UPG doub 380 n n C5 H5 UPG sing 381 n n C6 H6 UPG sing 382 n n C1C C2C UPG sing 383 n n C1C O4C UPG sing 384 n n C1C H1C UPG sing 385 n n C2C O2C UPG sing 386 n n C2C C3C UPG sing 387 n n C2C H2C UPG sing 388 n n O2C HO2C UPG sing 389 n n C3C C4C UPG sing 390 n n C3C O3C UPG sing 391 n n C3C H3C UPG sing 392 n n C4C O4C UPG sing 393 n n C4C C5C UPG sing 394 n n C4C H4C UPG sing 395 n n O3C HO3C UPG sing 396 n n C5C O5C UPG sing 397 n n C5C H5C1 UPG sing 398 n n C5C H5C2 UPG sing 399 n n O5C PA UPG sing 400 n n PA O1A UPG doub 401 n n PA O2A UPG sing 402 n n PA O3A UPG sing 403 n n O2A HOA2 UPG sing 404 n n O3A PB UPG sing 405 n n PB O1B UPG doub 406 n n PB O2B UPG sing 407 n n PB O3B UPG sing 408 n n O2B HOB2 UPG sing 409 n n O3B C1' UPG sing 410 n n C1' C2' UPG sing 411 n n C1' O5' UPG sing 412 n n C1' H1' UPG sing 413 n n C2' C3' UPG sing 414 n n C2' O2' UPG sing 415 n n C2' H2' UPG sing 416 n n C3' C4' UPG sing 417 n n C3' O3' UPG sing 418 n n C3' H3' UPG sing 419 n n C4' C5' UPG sing 420 n n C4' O4' UPG sing 421 n n C4' H4' UPG sing 422 n n C5' C6' UPG sing 423 n n C5' O5' UPG sing 424 n n C5' H5' UPG sing 425 n n C6' O6' UPG sing 426 n n C6' "H6'1" UPG sing 427 n n C6' "H6'2" UPG sing 428 n n O2' HO2' UPG sing 429 n n O3' HO3' UPG sing 430 n n O4' HO4' UPG sing 431 n n O6' HO6' UPG sing 432 n n # _atom_sites.entry_id 5JSX _atom_sites.fract_transf_matrix[1][1] 0.010124 _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] 0.010124 _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] 0.007817 _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 MN A 1 401 1 MN MN . C 3 UPG A 1 402 2 UPG UPG . D 4 GOL A 1 403 1 GOL GOL . E 5 HOH A 1 501 3 HOH HOH . E 5 HOH A 2 502 25 HOH HOH . E 5 HOH A 3 503 61 HOH HOH . E 5 HOH A 4 504 71 HOH HOH . E 5 HOH A 5 505 34 HOH HOH . E 5 HOH A 6 506 18 HOH HOH . E 5 HOH A 7 507 24 HOH HOH . E 5 HOH A 8 508 5 HOH HOH . E 5 HOH A 9 509 2 HOH HOH . E 5 HOH A 10 510 70 HOH HOH . E 5 HOH A 11 511 54 HOH HOH . E 5 HOH A 12 512 9 HOH HOH . E 5 HOH A 13 513 11 HOH HOH . E 5 HOH A 14 514 72 HOH HOH . E 5 HOH A 15 515 62 HOH HOH . E 5 HOH A 16 516 41 HOH HOH . E 5 HOH A 17 517 69 HOH HOH . E 5 HOH A 18 518 40 HOH HOH . E 5 HOH A 19 519 37 HOH HOH . E 5 HOH A 20 520 27 HOH HOH . E 5 HOH A 21 521 63 HOH HOH . E 5 HOH A 22 522 19 HOH HOH . E 5 HOH A 23 523 67 HOH HOH . E 5 HOH A 24 524 44 HOH HOH . E 5 HOH A 25 525 22 HOH HOH . E 5 HOH A 26 526 10 HOH HOH . E 5 HOH A 27 527 59 HOH HOH . E 5 HOH A 28 528 7 HOH HOH . E 5 HOH A 29 529 51 HOH HOH . E 5 HOH A 30 530 45 HOH HOH . E 5 HOH A 31 531 68 HOH HOH . E 5 HOH A 32 532 35 HOH HOH . E 5 HOH A 33 533 12 HOH HOH . E 5 HOH A 34 534 42 HOH HOH . E 5 HOH A 35 535 21 HOH HOH . E 5 HOH A 36 536 20 HOH HOH . E 5 HOH A 37 537 48 HOH HOH . E 5 HOH A 38 538 60 HOH HOH . E 5 HOH A 39 539 65 HOH HOH . E 5 HOH A 40 540 55 HOH HOH . E 5 HOH A 41 541 23 HOH HOH . E 5 HOH A 42 542 66 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 . . . C 3 14.903 -12.939 -28.625 1 53.63 ? N1 UPG 402 A 1 HETATM 2 C C2 UPG . . . C 3 15.564 -14.037 -28.06 1 61.68 ? C2 UPG 402 A 1 HETATM 3 N N3 UPG . . . C 3 14.866 -14.93 -27.325 1 61.49 ? N3 UPG 402 A 1 HETATM 4 C C4 UPG . . . C 3 13.547 -14.798 -27.151 1 61.93 ? C4 UPG 402 A 1 HETATM 5 C C5 UPG . . . C 3 12.872 -13.715 -27.732 1 56.98 ? C5 UPG 402 A 1 HETATM 6 C C6 UPG . . . C 3 13.585 -12.776 -28.451 1 57.14 ? C6 UPG 402 A 1 HETATM 7 O O2 UPG . . . C 3 16.812 -14.165 -28.244 1 57.04 ? O2 UPG 402 A 1 HETATM 8 O O4 UPG . . . C 3 12.907 -15.649 -26.485 1 59.83 ? O4 UPG 402 A 1 HETATM 9 C C1C UPG . . . C 3 15.67 -12 -29.421 1 55.83 ? C1C UPG 402 A 1 HETATM 10 C C2C UPG . . . C 3 15.136 -11.896 -30.869 1 56.18 ? C2C UPG 402 A 1 HETATM 11 O O2C UPG . . . C 3 15.74 -12.863 -31.757 1 52.74 ? O2C UPG 402 A 1 HETATM 12 C C3C UPG . . . C 3 15.439 -10.468 -31.26 1 58.46 ? C3C UPG 402 A 1 HETATM 13 C C4C UPG . . . C 3 15.45 -9.735 -29.919 1 58.82 ? C4C UPG 402 A 1 HETATM 14 O O4C UPG . . . C 3 15.47 -10.715 -28.886 1 57.7 ? O4C UPG 402 A 1 HETATM 15 O O3C UPG . . . C 3 16.784 -10.531 -31.752 1 54.45 ? O3C UPG 402 A 1 HETATM 16 C C5C UPG . . . C 3 14.233 -8.859 -29.681 1 56.05 ? C5C UPG 402 A 1 HETATM 17 O O5C UPG . . . C 3 13.064 -9.657 -29.824 1 55.23 ? O5C UPG 402 A 1 HETATM 18 P PA UPG . . . C 3 11.916 -9.067 -30.775 1 57.64 ? PA UPG 402 A 1 HETATM 19 O O1A UPG . . . C 3 12.584 -8.575 -32.072 1 63.35 ? O1A UPG 402 A 1 HETATM 20 O O2A UPG . . . C 3 10.894 -10.17 -31.076 1 54.7 ? O2A UPG 402 A 1 HETATM 21 O O3A UPG . . . C 3 11.362 -7.949 -29.804 1 64.65 ? O3A UPG 402 A 1 HETATM 22 P PB UPG . . . C 3 10.685 -6.598 -30.213 1 62.31 ? PB UPG 402 A 1 HETATM 23 O O1B UPG . . . C 3 9.223 -6.686 -30.464 1 62.88 ? O1B UPG 402 A 1 HETATM 24 O O2B UPG . . . C 3 11.468 -5.886 -31.333 1 64.17 ? O2B UPG 402 A 1 HETATM 25 O O3B UPG . . . C 3 10.858 -5.855 -28.826 1 61.01 ? O3B UPG 402 A 1 HETATM 26 C C1' UPG . . . C 3 11.503 -4.624 -28.601 1 63.82 ? C1' UPG 402 A 1 HETATM 27 C C2' UPG . . . C 3 13.019 -4.78 -28.634 1 63.15 ? C2' UPG 402 A 1 HETATM 28 C C3' UPG . . . C 3 13.343 -5.963 -27.789 1 61.65 ? C3' UPG 402 A 1 HETATM 29 C C4' UPG . . . C 3 12.88 -5.696 -26.403 1 60.61 ? C4' UPG 402 A 1 HETATM 30 C C5' UPG . . . C 3 11.39 -5.452 -26.41 1 57.51 ? C5' UPG 402 A 1 HETATM 31 C C6' UPG . . . C 3 10.889 -5.261 -24.97 1 57.44 ? C6' UPG 402 A 1 HETATM 32 O O2' UPG . . . C 3 13.595 -5.016 -29.943 1 62.08 ? O2' UPG 402 A 1 HETATM 33 O O3' UPG . . . C 3 14.744 -6.162 -27.755 1 55.62 ? O3' UPG 402 A 1 HETATM 34 O O4' UPG . . . C 3 13.185 -6.828 -25.615 1 64.4 ? O4' UPG 402 A 1 HETATM 35 O O5' UPG . . . C 3 11.107 -4.343 -27.283 1 63.46 ? O5' UPG 402 A 1 HETATM 36 O O6' UPG . . . C 3 11.933 -4.681 -24.129 1 55.46 ? O6' UPG 402 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #