data_4EDF # _model_server_result.job_id DOnrKSbPUNjUm0RQWAd0aQ _model_server_result.datetime_utc '2024-11-07 19:35:02' _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 4edf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4EDF # _exptl.entry_id 4EDF _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.01 _cell.angle_gamma 90 _cell.entry_id 4EDF _cell.length_a 88.66 _cell.length_b 151.07 _cell.length_c 88.74 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,D,E,H,I,L 1 1 B,C,F,G,J,K 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _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 4EDF _atom_sites.fract_transf_matrix[1][1] 0.011279 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003451 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006619 _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] 0.011784 _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 E 2 UPG A 1 501 501 UPG UPG . F 2 UPG B 1 501 501 UPG UPG . G 2 UPG C 1 501 501 UPG UPG . H 2 UPG D 1 501 501 UPG UPG . I 3 HOH A 1 601 2 HOH HOH . I 3 HOH A 2 602 3 HOH HOH . I 3 HOH A 3 603 6 HOH HOH . I 3 HOH A 4 604 8 HOH HOH . I 3 HOH A 5 605 11 HOH HOH . I 3 HOH A 6 606 13 HOH HOH . I 3 HOH A 7 607 15 HOH HOH . I 3 HOH A 8 608 16 HOH HOH . I 3 HOH A 9 609 19 HOH HOH . I 3 HOH A 10 610 20 HOH HOH . I 3 HOH A 11 611 26 HOH HOH . I 3 HOH A 12 612 30 HOH HOH . I 3 HOH A 13 613 35 HOH HOH . I 3 HOH A 14 614 37 HOH HOH . I 3 HOH A 15 615 49 HOH HOH . I 3 HOH A 16 616 50 HOH HOH . I 3 HOH A 17 617 51 HOH HOH . I 3 HOH A 18 618 52 HOH HOH . I 3 HOH A 19 619 55 HOH HOH . I 3 HOH A 20 620 56 HOH HOH . I 3 HOH A 21 621 59 HOH HOH . I 3 HOH A 22 622 69 HOH HOH . I 3 HOH A 23 623 74 HOH HOH . I 3 HOH A 24 624 89 HOH HOH . I 3 HOH A 25 625 90 HOH HOH . I 3 HOH A 26 626 93 HOH HOH . I 3 HOH A 27 627 96 HOH HOH . I 3 HOH A 28 628 97 HOH HOH . I 3 HOH A 29 629 99 HOH HOH . I 3 HOH A 30 630 110 HOH HOH . I 3 HOH A 31 631 117 HOH HOH . I 3 HOH A 32 632 125 HOH HOH . I 3 HOH A 33 633 131 HOH HOH . I 3 HOH A 34 634 134 HOH HOH . I 3 HOH A 35 635 143 HOH HOH . I 3 HOH A 36 636 153 HOH HOH . I 3 HOH A 37 637 157 HOH HOH . I 3 HOH A 38 638 165 HOH HOH . I 3 HOH A 39 639 166 HOH HOH . I 3 HOH A 40 640 169 HOH HOH . I 3 HOH A 41 641 176 HOH HOH . J 3 HOH B 1 601 4 HOH HOH . J 3 HOH B 2 602 12 HOH HOH . J 3 HOH B 3 603 29 HOH HOH . J 3 HOH B 4 604 33 HOH HOH . J 3 HOH B 5 605 36 HOH HOH . J 3 HOH B 6 606 39 HOH HOH . J 3 HOH B 7 607 44 HOH HOH . J 3 HOH B 8 608 45 HOH HOH . J 3 HOH B 9 609 61 HOH HOH . J 3 HOH B 10 610 62 HOH HOH . J 3 HOH B 11 611 64 HOH HOH . J 3 HOH B 12 612 66 HOH HOH . J 3 HOH B 13 613 67 HOH HOH . J 3 HOH B 14 614 82 HOH HOH . J 3 HOH B 15 615 85 HOH HOH . J 3 HOH B 16 616 91 HOH HOH . J 3 HOH B 17 617 92 HOH HOH . J 3 HOH B 18 618 103 HOH HOH . J 3 HOH B 19 619 105 HOH HOH . J 3 HOH B 20 620 113 HOH HOH . J 3 HOH B 21 621 118 HOH HOH . J 3 HOH B 22 622 120 HOH HOH . J 3 HOH B 23 623 129 HOH HOH . J 3 HOH B 24 624 132 HOH HOH . J 3 HOH B 25 625 150 HOH HOH . J 3 HOH B 26 626 151 HOH HOH . J 3 HOH B 27 627 152 HOH HOH . J 3 HOH B 28 628 159 HOH HOH . J 3 HOH B 29 629 161 HOH HOH . J 3 HOH B 30 630 164 HOH HOH . J 3 HOH B 31 631 171 HOH HOH . J 3 HOH B 32 632 174 HOH HOH . K 3 HOH C 1 601 17 HOH HOH . K 3 HOH C 2 602 18 HOH HOH . K 3 HOH C 3 603 21 HOH HOH . K 3 HOH C 4 604 24 HOH HOH . K 3 HOH C 5 605 25 HOH HOH . K 3 HOH C 6 606 28 HOH HOH . K 3 HOH C 7 607 31 HOH HOH . K 3 HOH C 8 608 34 HOH HOH . K 3 HOH C 9 609 43 HOH HOH . K 3 HOH C 10 610 47 HOH HOH . K 3 HOH C 11 611 58 HOH HOH . K 3 HOH C 12 612 63 HOH HOH . K 3 HOH C 13 613 65 HOH HOH . K 3 HOH C 14 614 70 HOH HOH . K 3 HOH C 15 615 78 HOH HOH . K 3 HOH C 16 616 80 HOH HOH . K 3 HOH C 17 617 81 HOH HOH . K 3 HOH C 18 618 87 HOH HOH . K 3 HOH C 19 619 100 HOH HOH . K 3 HOH C 20 620 101 HOH HOH . K 3 HOH C 21 621 107 HOH HOH . K 3 HOH C 22 622 111 HOH HOH . K 3 HOH C 23 623 116 HOH HOH . K 3 HOH C 24 624 119 HOH HOH . K 3 HOH C 25 625 121 HOH HOH . K 3 HOH C 26 626 122 HOH HOH . K 3 HOH C 27 627 123 HOH HOH . K 3 HOH C 28 628 130 HOH HOH . K 3 HOH C 29 629 137 HOH HOH . K 3 HOH C 30 630 139 HOH HOH . K 3 HOH C 31 631 145 HOH HOH . K 3 HOH C 32 632 146 HOH HOH . K 3 HOH C 33 633 163 HOH HOH . K 3 HOH C 34 634 167 HOH HOH . L 3 HOH D 1 601 7 HOH HOH . L 3 HOH D 2 602 9 HOH HOH . L 3 HOH D 3 603 14 HOH HOH . L 3 HOH D 4 604 22 HOH HOH . L 3 HOH D 5 605 23 HOH HOH . L 3 HOH D 6 606 38 HOH HOH . L 3 HOH D 7 607 40 HOH HOH . L 3 HOH D 8 608 42 HOH HOH . L 3 HOH D 9 609 46 HOH HOH . L 3 HOH D 10 610 53 HOH HOH . L 3 HOH D 11 611 54 HOH HOH . L 3 HOH D 12 612 57 HOH HOH . L 3 HOH D 13 613 72 HOH HOH . L 3 HOH D 14 614 73 HOH HOH . L 3 HOH D 15 615 77 HOH HOH . L 3 HOH D 16 616 79 HOH HOH . L 3 HOH D 17 617 83 HOH HOH . L 3 HOH D 18 618 84 HOH HOH . L 3 HOH D 19 619 86 HOH HOH . L 3 HOH D 20 620 95 HOH HOH . L 3 HOH D 21 621 108 HOH HOH . L 3 HOH D 22 622 109 HOH HOH . L 3 HOH D 23 623 114 HOH HOH . L 3 HOH D 24 624 115 HOH HOH . L 3 HOH D 25 625 124 HOH HOH . L 3 HOH D 26 626 126 HOH HOH . L 3 HOH D 27 627 127 HOH HOH . L 3 HOH D 28 628 128 HOH HOH . L 3 HOH D 29 629 136 HOH HOH . L 3 HOH D 30 630 138 HOH HOH . L 3 HOH D 31 631 140 HOH HOH . L 3 HOH D 32 632 148 HOH HOH . L 3 HOH D 33 633 149 HOH HOH . L 3 HOH D 34 634 154 HOH HOH . L 3 HOH D 35 635 155 HOH HOH . L 3 HOH D 36 636 156 HOH HOH . L 3 HOH D 37 637 172 HOH HOH . L 3 HOH D 38 638 173 HOH HOH . L 3 HOH D 39 639 175 HOH HOH . L 3 HOH D 40 640 177 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 . . . H 2 54.015 -20.212 19.193 1 20.99 ? N1 UPG 501 D 1 HETATM 2 C C2 UPG . . . H 2 53.203 -20.212 20.343 1 32.3 ? C2 UPG 501 D 1 HETATM 3 N N3 UPG . . . H 2 51.88 -20.382 20.226 1 29.22 ? N3 UPG 501 D 1 HETATM 4 C C4 UPG . . . H 2 51.314 -20.55 19.024 1 21.09 ? C4 UPG 501 D 1 HETATM 5 C C5 UPG . . . H 2 52.095 -20.554 17.876 1 21.96 ? C5 UPG 501 D 1 HETATM 6 C C6 UPG . . . H 2 53.469 -20.378 17.986 1 15.86 ? C6 UPG 501 D 1 HETATM 7 O O2 UPG . . . H 2 53.725 -20.055 21.471 1 27.72 ? O2 UPG 501 D 1 HETATM 8 O O4 UPG . . . H 2 50.079 -20.705 18.934 1 27.03 ? O4 UPG 501 D 1 HETATM 9 C C1C UPG . . . H 2 55.456 -20.028 19.338 1 22.37 ? C1C UPG 501 D 1 HETATM 10 C C2C UPG . . . H 2 56.247 -21.174 18.73 1 18.2 ? C2C UPG 501 D 1 HETATM 11 O O2C UPG . . . H 2 56.401 -22.272 19.628 1 26.71 ? O2C UPG 501 D 1 HETATM 12 C C3C UPG . . . H 2 57.564 -20.516 18.372 1 17.77 ? C3C UPG 501 D 1 HETATM 13 C C4C UPG . . . H 2 57.18 -19.075 18.068 1 22.33 ? C4C UPG 501 D 1 HETATM 14 O O4C UPG . . . H 2 55.867 -18.876 18.602 1 30.49 ? O4C UPG 501 D 1 HETATM 15 O O3C UPG . . . H 2 58.441 -20.52 19.505 1 19.56 ? O3C UPG 501 D 1 HETATM 16 C C5C UPG . . . H 2 57.158 -18.787 16.574 1 21.75 ? C5C UPG 501 D 1 HETATM 17 O O5C UPG . . . H 2 56.774 -19.974 15.885 1 20.6 ? O5C UPG 501 D 1 HETATM 18 P PA UPG . . . H 2 56.538 -19.954 14.301 1 23.02 ? PA UPG 501 D 1 HETATM 19 O O1A UPG . . . H 2 55.766 -21.204 13.952 1 24.79 ? O1A UPG 501 D 1 HETATM 20 O O2A UPG . . . H 2 55.948 -18.605 13.973 1 24.4 ? O2A UPG 501 D 1 HETATM 21 O O3A UPG . . . H 2 58.088 -20.15 13.85 1 22.94 ? O3A UPG 501 D 1 HETATM 22 P PB UPG . . . H 2 59.017 -19.181 12.945 1 25.35 ? PB UPG 501 D 1 HETATM 23 O O1B UPG . . . H 2 59.664 -18.149 13.842 1 40.37 ? O1B UPG 501 D 1 HETATM 24 O O2B UPG . . . H 2 59.919 -20.033 12.083 1 26.21 ? O2B UPG 501 D 1 HETATM 25 O O3B UPG . . . H 2 57.977 -18.443 11.961 1 25.08 ? O3B UPG 501 D 1 HETATM 26 C C1' UPG . . . H 2 57.77 -17.037 12.042 1 19.16 ? C1' UPG 501 D 1 HETATM 27 C C2' UPG . . . H 2 56.546 -16.684 11.204 1 18.88 ? C2' UPG 501 D 1 HETATM 28 C C3' UPG . . . H 2 56.827 -16.9 9.722 1 28.14 ? C3' UPG 501 D 1 HETATM 29 C C4' UPG . . . H 2 58.109 -16.178 9.348 1 27.89 ? C4' UPG 501 D 1 HETATM 30 C C5' UPG . . . H 2 59.254 -16.672 10.215 1 28.39 ? C5' UPG 501 D 1 HETATM 31 C C6' UPG . . . H 2 60.571 -16.029 9.8 1 25.03 ? C6' UPG 501 D 1 HETATM 32 O O2' UPG . . . H 2 55.426 -17.486 11.591 1 25.17 ? O2' UPG 501 D 1 HETATM 33 O O3' UPG . . . H 2 55.752 -16.375 8.936 1 34.7 ? O3' UPG 501 D 1 HETATM 34 O O4' UPG . . . H 2 58.408 -16.398 7.972 1 27.8 ? O4' UPG 501 D 1 HETATM 35 O O5' UPG . . . H 2 58.938 -16.354 11.568 1 23.56 ? O5' UPG 501 D 1 HETATM 36 O O6' UPG . . . H 2 60.43 -14.604 9.778 1 32.45 ? O6' UPG 501 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #