data_4Y6N # _model_server_result.job_id QsVBbN2X_BzP7i2o6ajvtQ _model_server_result.datetime_utc '2025-01-09 21:56:32' _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 4y6n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4Y6N # _exptl.entry_id 4Y6N _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 4Y6N _cell.length_a 98.73 _cell.length_b 98.73 _cell.length_c 127.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y6N _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc3 B MN MN . A MN 401 1_555 D O1A UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 B MN MN . A MN 401 1_555 D O2B UPG . A UPG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 B MN MN . A MN 401 1_555 G O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc6 B MN MN . A MN 401 1_555 G O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _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 384 n n N1 C6 UPG sing 385 n n N1 C1C UPG sing 386 n n C2 N3 UPG sing 387 n n C2 O2 UPG doub 388 n n N3 C4 UPG sing 389 n n N3 HN3 UPG sing 390 n n C4 C5 UPG sing 391 n n C4 O4 UPG doub 392 n n C5 C6 UPG doub 393 n n C5 H5 UPG sing 394 n n C6 H6 UPG sing 395 n n C1C C2C UPG sing 396 n n C1C O4C UPG sing 397 n n C1C H1C UPG sing 398 n n C2C O2C UPG sing 399 n n C2C C3C UPG sing 400 n n C2C H2C UPG sing 401 n n O2C HO2C UPG sing 402 n n C3C C4C UPG sing 403 n n C3C O3C UPG sing 404 n n C3C H3C UPG sing 405 n n C4C O4C UPG sing 406 n n C4C C5C UPG sing 407 n n C4C H4C UPG sing 408 n n O3C HO3C UPG sing 409 n n C5C O5C UPG sing 410 n n C5C H5C1 UPG sing 411 n n C5C H5C2 UPG sing 412 n n O5C PA UPG sing 413 n n PA O1A UPG doub 414 n n PA O2A UPG sing 415 n n PA O3A UPG sing 416 n n O2A HOA2 UPG sing 417 n n O3A PB UPG sing 418 n n PB O1B UPG doub 419 n n PB O2B UPG sing 420 n n PB O3B UPG sing 421 n n O2B HOB2 UPG sing 422 n n O3B C1' UPG sing 423 n n C1' C2' UPG sing 424 n n C1' O5' UPG sing 425 n n C1' H1' UPG sing 426 n n C2' C3' UPG sing 427 n n C2' O2' UPG sing 428 n n C2' H2' UPG sing 429 n n C3' C4' UPG sing 430 n n C3' O3' UPG sing 431 n n C3' H3' UPG sing 432 n n C4' C5' UPG sing 433 n n C4' O4' UPG sing 434 n n C4' H4' UPG sing 435 n n C5' C6' UPG sing 436 n n C5' O5' UPG sing 437 n n C5' H5' UPG sing 438 n n C6' O6' UPG sing 439 n n C6' "H6'1" UPG sing 440 n n C6' "H6'2" UPG sing 441 n n O2' HO2' UPG sing 442 n n O3' HO3' UPG sing 443 n n O4' HO4' UPG sing 444 n n O6' HO6' UPG sing 445 n n # _atom_sites.entry_id 4Y6N _atom_sites.fract_transf_matrix[1][1] 0.010129 _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] 0.010129 _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] 0.007839 _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 3PG A 1 402 1 3PG 3PG . D 4 UPG A 1 403 2 UPG UPG . E 5 EDO A 1 404 1 EDO EDO . F 5 EDO A 1 405 1 EDO EDO . G 6 HOH A 1 501 100 HOH HOH . G 6 HOH A 2 502 2 HOH HOH . G 6 HOH A 3 503 25 HOH HOH . G 6 HOH A 4 504 4 HOH HOH . G 6 HOH A 5 505 13 HOH HOH . G 6 HOH A 6 506 5 HOH HOH . G 6 HOH A 7 507 8 HOH HOH . G 6 HOH A 8 508 12 HOH HOH . G 6 HOH A 9 509 1 HOH HOH . G 6 HOH A 10 510 67 HOH HOH . G 6 HOH A 11 511 41 HOH HOH . G 6 HOH A 12 512 9 HOH HOH . G 6 HOH A 13 513 14 HOH HOH . G 6 HOH A 14 514 90 HOH HOH . G 6 HOH A 15 515 46 HOH HOH . G 6 HOH A 16 516 45 HOH HOH . G 6 HOH A 17 517 21 HOH HOH . G 6 HOH A 18 518 10 HOH HOH . G 6 HOH A 19 519 51 HOH HOH . G 6 HOH A 20 520 20 HOH HOH . G 6 HOH A 21 521 30 HOH HOH . G 6 HOH A 22 522 27 HOH HOH . G 6 HOH A 23 523 53 HOH HOH . G 6 HOH A 24 524 11 HOH HOH . G 6 HOH A 25 525 29 HOH HOH . G 6 HOH A 26 526 17 HOH HOH . G 6 HOH A 27 527 42 HOH HOH . G 6 HOH A 28 528 7 HOH HOH . G 6 HOH A 29 529 101 HOH HOH . G 6 HOH A 30 530 75 HOH HOH . G 6 HOH A 31 531 24 HOH HOH . G 6 HOH A 32 532 63 HOH HOH . G 6 HOH A 33 533 82 HOH HOH . G 6 HOH A 34 534 59 HOH HOH . G 6 HOH A 35 535 78 HOH HOH . G 6 HOH A 36 536 64 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 14.8 -13.192 -27.687 0.88 71.31 ? N1 UPG 403 A 1 HETATM 2 C C2 UPG . . . D 4 15.398 -14.254 -26.979 0.88 82 ? C2 UPG 403 A 1 HETATM 3 N N3 UPG . . . D 4 14.631 -15.091 -26.262 0.88 77.75 ? N3 UPG 403 A 1 HETATM 4 C C4 UPG . . . D 4 13.305 -14.938 -26.207 0.88 76.88 ? C4 UPG 403 A 1 HETATM 5 C C5 UPG . . . D 4 12.69 -13.893 -26.892 0.88 77.49 ? C5 UPG 403 A 1 HETATM 6 C C6 UPG . . . D 4 13.47 -13.011 -27.626 0.88 73.76 ? C6 UPG 403 A 1 HETATM 7 O O2 UPG . . . D 4 16.64 -14.413 -27.027 0.88 74.43 ? O2 UPG 403 A 1 HETATM 8 O O4 UPG . . . D 4 12.632 -15.747 -25.534 0.88 87.4 ? O4 UPG 403 A 1 HETATM 9 C C1C UPG . . . D 4 15.651 -12.273 -28.44 0.88 73.8 ? C1C UPG 403 A 1 HETATM 10 C C2C UPG . . . D 4 15.258 -12.133 -29.906 0.88 72.37 ? C2C UPG 403 A 1 HETATM 11 O O2C UPG . . . D 4 15.925 -13.132 -30.673 0.88 76.26 ? O2C UPG 403 A 1 HETATM 12 C C3C UPG . . . D 4 15.743 -10.743 -30.221 0.88 78.3 ? C3C UPG 403 A 1 HETATM 13 C C4C UPG . . . D 4 15.679 -10.001 -28.894 0.88 82.65 ? C4C UPG 403 A 1 HETATM 14 O O4C UPG . . . D 4 15.562 -10.974 -27.861 0.88 75.36 ? O4C UPG 403 A 1 HETATM 15 O O3C UPG . . . D 4 17.106 -10.772 -30.659 0.88 74 ? O3C UPG 403 A 1 HETATM 16 C C5C UPG . . . D 4 14.492 -9.058 -28.825 0.88 86.61 ? C5C UPG 403 A 1 HETATM 17 O O5C UPG . . . D 4 13.293 -9.82 -28.928 0.88 73.69 ? O5C UPG 403 A 1 HETATM 18 P PA UPG . . . D 4 12.068 -9.263 -29.808 0.88 78.65 ? PA UPG 403 A 1 HETATM 19 O O1A UPG . . . D 4 12.553 -8.766 -31.157 0.88 85.56 ? O1A UPG 403 A 1 HETATM 20 O O2A UPG . . . D 4 11.046 -10.363 -29.985 0.88 73.18 ? O2A UPG 403 A 1 HETATM 21 O O3A UPG . . . D 4 11.503 -8.059 -28.901 0.88 95.73 ? O3A UPG 403 A 1 HETATM 22 P PB UPG . . . D 4 10.903 -6.668 -29.476 0.88 87.12 ? PB UPG 403 A 1 HETATM 23 O O1B UPG . . . D 4 9.518 -6.915 -30.021 0.88 88.98 ? O1B UPG 403 A 1 HETATM 24 O O2B UPG . . . D 4 11.791 -5.997 -30.51 0.88 92.66 ? O2B UPG 403 A 1 HETATM 25 O O3B UPG . . . D 4 10.832 -5.812 -28.11 0.88 95.5 ? O3B UPG 403 A 1 HETATM 26 C C1' UPG . . . D 4 11.547 -4.618 -27.735 0.88 111.48 ? C1' UPG 403 A 1 HETATM 27 C C2' UPG . . . D 4 13.048 -4.808 -27.73 0.88 107.76 ? C2' UPG 403 A 1 HETATM 28 C C3' UPG . . . D 4 13.367 -6.007 -26.849 0.88 88.86 ? C3' UPG 403 A 1 HETATM 29 C C4' UPG . . . D 4 12.767 -5.846 -25.463 0.88 105.99 ? C4' UPG 403 A 1 HETATM 30 C C5' UPG . . . D 4 11.294 -5.448 -25.527 0.88 97.52 ? C5' UPG 403 A 1 HETATM 31 C C6' UPG . . . D 4 10.737 -5.149 -24.136 0.88 98.8 ? C6' UPG 403 A 1 HETATM 32 O O2' UPG . . . D 4 13.519 -4.95 -29.082 0.88 98.65 ? O2' UPG 403 A 1 HETATM 33 O O3' UPG . . . D 4 14.782 -6.103 -26.761 0.88 88.92 ? O3' UPG 403 A 1 HETATM 34 O O4' UPG . . . D 4 12.884 -7.064 -24.703 0.88 109.29 ? O4' UPG 403 A 1 HETATM 35 O O5' UPG . . . D 4 11.137 -4.314 -26.396 0.88 101.23 ? O5' UPG 403 A 1 HETATM 36 O O6' UPG . . . D 4 11.777 -4.739 -23.23 0.88 79.85 ? O6' UPG 403 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 36 #