data_7U2P # _model_server_result.job_id 0uWxqDN4FR3Wp4xxRG2hRg _model_server_result.datetime_utc '2024-12-04 16:45:28' _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 7u2p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 7U2P # _exptl.entry_id 7U2P _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 7U2P _cell.length_a 114.641 _cell.length_b 122.798 _cell.length_c 127.474 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U2P _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,F,G,H,I _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 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 288 A ASP 287 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 A OE1 GLU 515 A GLU 514 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc3 C O1A UPG . A UPG 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? metalc ? metalc4 C O1B UPG . A UPG 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc5 D MN MN . A MN 602 1_555 H O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 D MN MN . A MN 602 1_555 H O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B OG1 THR 24 B THR 19 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc8 F O3B GDP . B GDP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? metalc ? metalc9 G MG MG . B MG 202 1_555 I O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc10 G MG MG . B MG 202 1_555 I O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc11 G MG MG . B MG 202 1_555 I O HOH . B HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc12 G MG MG . B MG 202 1_555 I O HOH . B HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 407 n n N1 C6 UPG sing 408 n n N1 C1C UPG sing 409 n n C2 N3 UPG sing 410 n n C2 O2 UPG doub 411 n n N3 C4 UPG sing 412 n n N3 HN3 UPG sing 413 n n C4 C5 UPG sing 414 n n C4 O4 UPG doub 415 n n C5 C6 UPG doub 416 n n C5 H5 UPG sing 417 n n C6 H6 UPG sing 418 n n C1C C2C UPG sing 419 n n C1C O4C UPG sing 420 n n C1C H1C UPG sing 421 n n C2C O2C UPG sing 422 n n C2C C3C UPG sing 423 n n C2C H2C UPG sing 424 n n O2C HO2C UPG sing 425 n n C3C C4C UPG sing 426 n n C3C O3C UPG sing 427 n n C3C H3C UPG sing 428 n n C4C O4C UPG sing 429 n n C4C C5C UPG sing 430 n n C4C H4C UPG sing 431 n n O3C HO3C UPG sing 432 n n C5C O5C UPG sing 433 n n C5C H5C1 UPG sing 434 n n C5C H5C2 UPG sing 435 n n O5C PA UPG sing 436 n n PA O1A UPG doub 437 n n PA O2A UPG sing 438 n n PA O3A UPG sing 439 n n O2A HOA2 UPG sing 440 n n O3A PB UPG sing 441 n n PB O1B UPG doub 442 n n PB O2B UPG sing 443 n n PB O3B UPG sing 444 n n O2B HOB2 UPG sing 445 n n O3B C1' UPG sing 446 n n C1' C2' UPG sing 447 n n C1' O5' UPG sing 448 n n C1' H1' UPG sing 449 n n C2' C3' UPG sing 450 n n C2' O2' UPG sing 451 n n C2' H2' UPG sing 452 n n C3' C4' UPG sing 453 n n C3' O3' UPG sing 454 n n C3' H3' UPG sing 455 n n C4' C5' UPG sing 456 n n C4' O4' UPG sing 457 n n C4' H4' UPG sing 458 n n C5' C6' UPG sing 459 n n C5' O5' UPG sing 460 n n C5' H5' UPG sing 461 n n C6' O6' UPG sing 462 n n C6' "H6'1" UPG sing 463 n n C6' "H6'2" UPG sing 464 n n O2' HO2' UPG sing 465 n n O3' HO3' UPG sing 466 n n O4' HO4' UPG sing 467 n n O6' HO6' UPG sing 468 n n # _atom_sites.entry_id 7U2P _atom_sites.fract_transf_matrix[1][1] 0.008723 _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] 0.008143 _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] 0.007845 _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 1 601 601 UPG UPG . D 4 MN A 1 602 551 MN MN . E 5 SO4 A 1 603 1 SO4 SO4 . F 6 GDP B 1 201 201 GDP GDP . G 7 MG B 1 202 1 MG MG . H 8 HOH A 1 701 40 HOH HOH . H 8 HOH A 2 702 24 HOH HOH . H 8 HOH A 3 703 14 HOH HOH . H 8 HOH A 4 704 49 HOH HOH . H 8 HOH A 5 705 31 HOH HOH . H 8 HOH A 6 706 11 HOH HOH . H 8 HOH A 7 707 1 HOH HOH . H 8 HOH A 8 708 9 HOH HOH . H 8 HOH A 9 709 12 HOH HOH . H 8 HOH A 10 710 46 HOH HOH . H 8 HOH A 11 711 21 HOH HOH . H 8 HOH A 12 712 34 HOH HOH . H 8 HOH A 13 713 27 HOH HOH . H 8 HOH A 14 714 20 HOH HOH . H 8 HOH A 15 715 3 HOH HOH . H 8 HOH A 16 716 45 HOH HOH . H 8 HOH A 17 717 4 HOH HOH . H 8 HOH A 18 718 29 HOH HOH . H 8 HOH A 19 719 13 HOH HOH . H 8 HOH A 20 720 32 HOH HOH . H 8 HOH A 21 721 16 HOH HOH . H 8 HOH A 22 722 17 HOH HOH . H 8 HOH A 23 723 15 HOH HOH . H 8 HOH A 24 724 10 HOH HOH . H 8 HOH A 25 725 25 HOH HOH . H 8 HOH A 26 726 33 HOH HOH . H 8 HOH A 27 727 38 HOH HOH . H 8 HOH A 28 728 28 HOH HOH . H 8 HOH A 29 729 42 HOH HOH . H 8 HOH A 30 730 26 HOH HOH . H 8 HOH A 31 731 19 HOH HOH . H 8 HOH A 32 732 18 HOH HOH . H 8 HOH A 33 733 23 HOH HOH . H 8 HOH A 34 734 43 HOH HOH . H 8 HOH A 35 735 37 HOH HOH . H 8 HOH A 36 736 2 HOH HOH . H 8 HOH A 37 737 7 HOH HOH . H 8 HOH A 38 738 39 HOH HOH . H 8 HOH A 39 739 35 HOH HOH . H 8 HOH A 40 740 48 HOH HOH . H 8 HOH A 41 741 5 HOH HOH . H 8 HOH A 42 742 44 HOH HOH . I 8 HOH B 1 301 53 HOH HOH . I 8 HOH B 2 302 41 HOH HOH . I 8 HOH B 3 303 8 HOH HOH . I 8 HOH B 4 304 30 HOH HOH . I 8 HOH B 5 305 47 HOH HOH . I 8 HOH B 6 306 36 HOH HOH . I 8 HOH B 7 307 50 HOH HOH . I 8 HOH B 8 308 22 HOH HOH . I 8 HOH B 9 309 52 HOH HOH . I 8 HOH B 10 310 51 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 -22.851 -17.41 14.39 1 46.95 ? N1 UPG 601 A 1 HETATM 2 C C2 UPG . . . C 3 -21.824 -16.597 15.037 1 46.59 ? C2 UPG 601 A 1 HETATM 3 N N3 UPG . . . C 3 -21.403 -15.357 14.372 1 48.44 ? N3 UPG 601 A 1 HETATM 4 C C4 UPG . . . C 3 -21.994 -14.973 13.117 1 47.97 ? C4 UPG 601 A 1 HETATM 5 C C5 UPG . . . C 3 -23.027 -15.795 12.46 1 42.26 ? C5 UPG 601 A 1 HETATM 6 C C6 UPG . . . C 3 -23.432 -17.024 13.12 1 44.81 ? C6 UPG 601 A 1 HETATM 7 O O2 UPG . . . C 3 -21.35 -16.935 16.08 1 51.04 ? O2 UPG 601 A 1 HETATM 8 O O4 UPG . . . C 3 -21.631 -13.965 12.628 1 55.07 ? O4 UPG 601 A 1 HETATM 9 C C1C UPG . . . C 3 -23.209 -18.635 15.063 1 49.57 ? C1C UPG 601 A 1 HETATM 10 C C2C UPG . . . C 3 -24.35 -18.332 16.097 1 49.09 ? C2C UPG 601 A 1 HETATM 11 O O2C UPG . . . C 3 -24.192 -19.197 17.079 1 51.59 ? O2C UPG 601 A 1 HETATM 12 C C3C UPG . . . C 3 -25.624 -18.569 15.284 1 52.61 ? C3C UPG 601 A 1 HETATM 13 C C4C UPG . . . C 3 -25.209 -19.566 14.439 1 52.43 ? C4C UPG 601 A 1 HETATM 14 O O4C UPG . . . C 3 -23.615 -19.486 14.164 1 52.45 ? O4C UPG 601 A 1 HETATM 15 O O3C UPG . . . C 3 -26.6 -19.179 16.202 1 51.3 ? O3C UPG 601 A 1 HETATM 16 C C5C UPG . . . C 3 -25.983 -20.122 13.264 1 48.87 ? C5C UPG 601 A 1 HETATM 17 O O5C UPG . . . C 3 -27.312 -19.782 13.394 1 50.25 ? O5C UPG 601 A 1 HETATM 18 P PA UPG . . . C 3 -28.017 -19.653 11.974 1 50.39 ? PA UPG 601 A 1 HETATM 19 O O1A UPG . . . C 3 -29.502 -19.56 12.275 1 63.35 ? O1A UPG 601 A 1 HETATM 20 O O2A UPG . . . C 3 -27.572 -18.454 11.256 1 54.83 ? O2A UPG 601 A 1 HETATM 21 O O3A UPG . . . C 3 -27.747 -21.042 11.142 1 57.02 ? O3A UPG 601 A 1 HETATM 22 P PB UPG . . . C 3 -28.979 -22.009 10.685 1 50.46 ? PB UPG 601 A 1 HETATM 23 O O1B UPG . . . C 3 -30.092 -21.968 11.688 1 53.43 ? O1B UPG 601 A 1 HETATM 24 O O2B UPG . . . C 3 -29.414 -21.396 9.396 1 49.33 ? O2B UPG 601 A 1 HETATM 25 O O3B UPG . . . C 3 -28.33 -23.512 10.437 1 54.08 ? O3B UPG 601 A 1 HETATM 26 C C1' UPG . . . C 3 -28.514 -24.705 11.146 0.19 57.08 ? C1' UPG 601 A 1 HETATM 27 C C2' UPG . . . C 3 -27.926 -24.718 12.558 0.77 58.72 ? C2' UPG 601 A 1 HETATM 28 C C3' UPG . . . C 3 -26.601 -24.038 12.582 0.09 62.33 ? C3' UPG 601 A 1 HETATM 29 C C4' UPG . . . C 3 -25.736 -24.922 11.739 1 66.54 ? C4' UPG 601 A 1 HETATM 30 C C5' UPG . . . C 3 -26.285 -25.399 10.36 0.32 61.99 ? C5' UPG 601 A 1 HETATM 31 C C6' UPG . . . C 3 -25.451 -26.597 9.96 0.29 59.93 ? C6' UPG 601 A 1 HETATM 32 O O2' UPG . . . C 3 -28.846 -24.161 13.524 0.55 59.32 ? O2' UPG 601 A 1 HETATM 33 O O3' UPG . . . C 3 -26.094 -24.096 13.928 1 61 ? O3' UPG 601 A 1 HETATM 34 O O4' UPG . . . C 3 -24.277 -24.47 11.764 1 74.04 ? O4' UPG 601 A 1 HETATM 35 O O5' UPG . . . C 3 -27.743 -25.776 10.427 1 55.77 ? O5' UPG 601 A 1 HETATM 36 O O6' UPG . . . C 3 -24.119 -26.28 10.403 1 55.9 ? O6' UPG 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #