data_4Y7F # _model_server_result.job_id 3wms-zbKhsNVEoHlQKfe-A _model_server_result.datetime_utc '2024-11-22 11:03:17' _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 4y7f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4Y7F # _exptl.entry_id 4Y7F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 4 _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 4Y7F _cell.length_a 97.94 _cell.length_b 97.94 _cell.length_c 126.78 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y7F _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,F,G _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 4 _struct_asym.id D _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc3 B MN MN . A MN 401 1_555 D O1A UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc4 B MN MN . A MN 401 1_555 D O2B UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc5 B MN MN . A MN 401 1_555 G O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc6 B MN MN . A MN 401 1_555 G O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? # _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 387 n n N1 C6 UPG sing 388 n n N1 C1C UPG sing 389 n n C2 N3 UPG sing 390 n n C2 O2 UPG doub 391 n n N3 C4 UPG sing 392 n n N3 HN3 UPG sing 393 n n C4 C5 UPG sing 394 n n C4 O4 UPG doub 395 n n C5 C6 UPG doub 396 n n C5 H5 UPG sing 397 n n C6 H6 UPG sing 398 n n C1C C2C UPG sing 399 n n C1C O4C UPG sing 400 n n C1C H1C UPG sing 401 n n C2C O2C UPG sing 402 n n C2C C3C UPG sing 403 n n C2C H2C UPG sing 404 n n O2C HO2C UPG sing 405 n n C3C C4C UPG sing 406 n n C3C O3C UPG sing 407 n n C3C H3C UPG sing 408 n n C4C O4C UPG sing 409 n n C4C C5C UPG sing 410 n n C4C H4C UPG sing 411 n n O3C HO3C UPG sing 412 n n C5C O5C UPG sing 413 n n C5C H5C1 UPG sing 414 n n C5C H5C2 UPG sing 415 n n O5C PA UPG sing 416 n n PA O1A UPG doub 417 n n PA O2A UPG sing 418 n n PA O3A UPG sing 419 n n O2A HOA2 UPG sing 420 n n O3A PB UPG sing 421 n n PB O1B UPG doub 422 n n PB O2B UPG sing 423 n n PB O3B UPG sing 424 n n O2B HOB2 UPG sing 425 n n O3B C1' UPG sing 426 n n C1' C2' UPG sing 427 n n C1' O5' UPG sing 428 n n C1' H1' UPG sing 429 n n C2' C3' UPG sing 430 n n C2' O2' UPG sing 431 n n C2' H2' UPG sing 432 n n C3' C4' UPG sing 433 n n C3' O3' UPG sing 434 n n C3' H3' UPG sing 435 n n C4' C5' UPG sing 436 n n C4' O4' UPG sing 437 n n C4' H4' UPG sing 438 n n C5' C6' UPG sing 439 n n C5' O5' UPG sing 440 n n C5' H5' UPG sing 441 n n C6' O6' UPG sing 442 n n C6' "H6'1" UPG sing 443 n n C6' "H6'2" UPG sing 444 n n O2' HO2' UPG sing 445 n n O3' HO3' UPG sing 446 n n O4' HO4' UPG sing 447 n n O6' HO6' UPG sing 448 n n # _atom_sites.entry_id 4Y7F _atom_sites.fract_transf_matrix[1][1] 0.01021 _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] 0.01021 _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] 0.007888 _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 48X A 1 402 1 48X PPA . D 4 UPG A 1 403 2 UPG UPG . E 5 SO4 A 1 404 4 SO4 SO4 . F 6 EDO A 1 405 1 EDO EDO . G 7 HOH A 1 501 37 HOH HOH . G 7 HOH A 2 502 34 HOH HOH . G 7 HOH A 3 503 29 HOH HOH . G 7 HOH A 4 504 39 HOH HOH . G 7 HOH A 5 505 2 HOH HOH . G 7 HOH A 6 506 1 HOH HOH . G 7 HOH A 7 507 3 HOH HOH . G 7 HOH A 8 508 5 HOH HOH . G 7 HOH A 9 509 8 HOH HOH . G 7 HOH A 10 510 10 HOH HOH . G 7 HOH A 11 511 11 HOH HOH . G 7 HOH A 12 512 14 HOH HOH . G 7 HOH A 13 513 16 HOH HOH . G 7 HOH A 14 514 23 HOH HOH . G 7 HOH A 15 515 24 HOH HOH . G 7 HOH A 16 516 25 HOH HOH . G 7 HOH A 17 517 26 HOH HOH . G 7 HOH A 18 518 27 HOH HOH . G 7 HOH A 19 519 28 HOH HOH . G 7 HOH A 20 520 31 HOH HOH . G 7 HOH A 21 521 32 HOH HOH . G 7 HOH A 22 522 33 HOH HOH . G 7 HOH A 23 523 35 HOH HOH . G 7 HOH A 24 524 36 HOH HOH . G 7 HOH A 25 525 38 HOH HOH . G 7 HOH A 26 526 40 HOH HOH . G 7 HOH A 27 527 42 HOH HOH . G 7 HOH A 28 528 43 HOH HOH . G 7 HOH A 29 529 44 HOH HOH . G 7 HOH A 30 530 46 HOH HOH . G 7 HOH A 31 531 47 HOH HOH . G 7 HOH A 32 532 48 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 . . . D 4 14.849 -12.923 -27.726 1 48.85 ? N1 UPG 403 A 1 HETATM 2 C C2 UPG . . . D 4 15.441 -14.023 -27.089 1 56.9 ? C2 UPG 403 A 1 HETATM 3 N N3 UPG . . . D 4 14.676 -14.875 -26.409 1 56.71 ? N3 UPG 403 A 1 HETATM 4 C C4 UPG . . . D 4 13.362 -14.723 -26.307 1 57.15 ? C4 UPG 403 A 1 HETATM 5 C C5 UPG . . . D 4 12.751 -13.651 -26.924 1 52.2 ? C5 UPG 403 A 1 HETATM 6 C C6 UPG . . . D 4 13.526 -12.749 -27.632 1 52.36 ? C6 UPG 403 A 1 HETATM 7 O O2 UPG . . . D 4 16.675 -14.216 -27.155 1 52.26 ? O2 UPG 403 A 1 HETATM 8 O O4 UPG . . . D 4 12.707 -15.561 -25.65 1 55.05 ? O4 UPG 403 A 1 HETATM 9 C C1C UPG . . . D 4 15.688 -11.976 -28.472 1 51.05 ? C1C UPG 403 A 1 HETATM 10 C C2C UPG . . . D 4 15.251 -11.833 -29.922 1 51.4 ? C2C UPG 403 A 1 HETATM 11 O O2C UPG . . . D 4 16.005 -12.696 -30.773 1 47.96 ? O2C UPG 403 A 1 HETATM 12 C C3C UPG . . . D 4 15.489 -10.378 -30.244 1 53.68 ? C3C UPG 403 A 1 HETATM 13 C C4C UPG . . . D 4 15.536 -9.685 -28.895 1 54.04 ? C4C UPG 403 A 1 HETATM 14 O O4C UPG . . . D 4 15.575 -10.687 -27.886 1 52.92 ? O4C UPG 403 A 1 HETATM 15 O O3C UPG . . . D 4 16.733 -10.194 -30.92 1 49.67 ? O3C UPG 403 A 1 HETATM 16 C C5C UPG . . . D 4 14.313 -8.817 -28.659 1 51.27 ? C5C UPG 403 A 1 HETATM 17 O O5C UPG . . . D 4 13.139 -9.614 -28.746 1 50.45 ? O5C UPG 403 A 1 HETATM 18 P PA UPG . . . D 4 11.943 -9.061 -29.666 1 52.86 ? PA UPG 403 A 1 HETATM 19 O O1A UPG . . . D 4 12.448 -8.533 -30.985 1 58.57 ? O1A UPG 403 A 1 HETATM 20 O O2A UPG . . . D 4 10.97 -10.195 -29.903 1 49.92 ? O2A UPG 403 A 1 HETATM 21 O O3A UPG . . . D 4 11.341 -7.859 -28.786 1 59.87 ? O3A UPG 403 A 1 HETATM 22 P PB UPG . . . D 4 10.828 -6.429 -29.335 1 57.53 ? PB UPG 403 A 1 HETATM 23 O O1B UPG . . . D 4 9.462 -6.498 -29.976 1 58.1 ? O1B UPG 403 A 1 HETATM 24 O O2B UPG . . . D 4 11.786 -5.748 -30.271 1 59.39 ? O2B UPG 403 A 1 HETATM 25 O O3B UPG . . . D 4 10.742 -5.664 -27.93 1 56.23 ? O3B UPG 403 A 1 HETATM 26 C C1' UPG . . . D 4 11.311 -4.411 -27.565 1 59.04 ? C1' UPG 403 A 1 HETATM 27 C C2' UPG . . . D 4 12.826 -4.39 -27.639 1 58.37 ? C2' UPG 403 A 1 HETATM 28 C C3' UPG . . . D 4 13.337 -5.68 -27.006 1 56.87 ? C3' UPG 403 A 1 HETATM 29 C C4' UPG . . . D 4 12.872 -5.707 -25.561 1 55.83 ? C4' UPG 403 A 1 HETATM 30 C C5' UPG . . . D 4 11.381 -5.394 -25.407 1 52.73 ? C5' UPG 403 A 1 HETATM 31 C C6' UPG . . . D 4 10.968 -5.165 -23.955 1 52.66 ? C6' UPG 403 A 1 HETATM 32 O O2' UPG . . . D 4 13.243 -4.134 -28.985 1 57.3 ? O2' UPG 403 A 1 HETATM 33 O O3' UPG . . . D 4 14.759 -5.753 -27 1 50.84 ? O3' UPG 403 A 1 HETATM 34 O O4' UPG . . . D 4 13.118 -7.008 -25.023 1 59.62 ? O4' UPG 403 A 1 HETATM 35 O O5' UPG . . . D 4 11.013 -4.24 -26.182 1 58.68 ? O5' UPG 403 A 1 HETATM 36 O O6' UPG . . . D 4 12.091 -4.933 -23.103 1 50.68 ? O6' UPG 403 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #