data_4Y9X # _model_server_result.job_id oP4rp3THMDfQ6-5KLqNIxw _model_server_result.datetime_utc '2025-01-10 06:05:06' _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 4y9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4Y9X # _exptl.entry_id 4Y9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 5 _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 4Y9X _cell.length_a 98.85 _cell.length_b 98.85 _cell.length_c 127.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y9X _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 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 1,2 # 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 5 _struct_asym.id E _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc3 B MN MN . A MN 401 1_555 E O1A UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc4 B MN MN . A MN 401 1_555 E O2B UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc5 B MN MN . A MN 401 1_555 I O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B MN MN . A MN 401 1_555 I O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? # _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 4Y9X _atom_sites.fract_transf_matrix[1][1] 0.010116 _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] 0.010116 _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] 0.007825 _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 CL A 1 402 2 CL CL . D 4 3PG A 1 403 1 3PG 3PG . E 5 UPG A 1 404 2 UPG UPG . F 6 EDO A 1 405 4 EDO EDO . G 6 EDO A 1 406 5 EDO EDO . H 6 EDO A 1 407 1 EDO EDO . I 7 HOH A 1 501 46 HOH HOH . I 7 HOH A 2 502 53 HOH HOH . I 7 HOH A 3 503 73 HOH HOH . I 7 HOH A 4 504 36 HOH HOH . I 7 HOH A 5 505 84 HOH HOH . I 7 HOH A 6 506 88 HOH HOH . I 7 HOH A 7 507 8 HOH HOH . I 7 HOH A 8 508 1 HOH HOH . I 7 HOH A 9 509 2 HOH HOH . I 7 HOH A 10 510 3 HOH HOH . I 7 HOH A 11 511 5 HOH HOH . I 7 HOH A 12 512 6 HOH HOH . I 7 HOH A 13 513 7 HOH HOH . I 7 HOH A 14 514 9 HOH HOH . I 7 HOH A 15 515 10 HOH HOH . I 7 HOH A 16 516 11 HOH HOH . I 7 HOH A 17 517 12 HOH HOH . I 7 HOH A 18 518 13 HOH HOH . I 7 HOH A 19 519 14 HOH HOH . I 7 HOH A 20 520 15 HOH HOH . I 7 HOH A 21 521 16 HOH HOH . I 7 HOH A 22 522 17 HOH HOH . I 7 HOH A 23 523 18 HOH HOH . I 7 HOH A 24 524 20 HOH HOH . I 7 HOH A 25 525 23 HOH HOH . I 7 HOH A 26 526 24 HOH HOH . I 7 HOH A 27 527 26 HOH HOH . I 7 HOH A 28 528 29 HOH HOH . I 7 HOH A 29 529 30 HOH HOH . I 7 HOH A 30 530 32 HOH HOH . I 7 HOH A 31 531 34 HOH HOH . I 7 HOH A 32 532 35 HOH HOH . I 7 HOH A 33 533 37 HOH HOH . I 7 HOH A 34 534 38 HOH HOH . I 7 HOH A 35 535 39 HOH HOH . I 7 HOH A 36 536 40 HOH HOH . I 7 HOH A 37 537 41 HOH HOH . I 7 HOH A 38 538 42 HOH HOH . I 7 HOH A 39 539 44 HOH HOH . I 7 HOH A 40 540 50 HOH HOH . I 7 HOH A 41 541 51 HOH HOH . I 7 HOH A 42 542 52 HOH HOH . I 7 HOH A 43 543 54 HOH HOH . I 7 HOH A 44 544 56 HOH HOH . I 7 HOH A 45 545 59 HOH HOH . I 7 HOH A 46 546 60 HOH HOH . I 7 HOH A 47 547 61 HOH HOH . I 7 HOH A 48 548 62 HOH HOH . I 7 HOH A 49 549 64 HOH HOH . I 7 HOH A 50 550 65 HOH HOH . I 7 HOH A 51 551 66 HOH HOH . I 7 HOH A 52 552 67 HOH HOH . I 7 HOH A 53 553 68 HOH HOH . I 7 HOH A 54 554 69 HOH HOH . I 7 HOH A 55 555 70 HOH HOH . I 7 HOH A 56 556 71 HOH HOH . I 7 HOH A 57 557 74 HOH HOH . I 7 HOH A 58 558 75 HOH HOH . I 7 HOH A 59 559 79 HOH HOH . I 7 HOH A 60 560 81 HOH HOH . I 7 HOH A 61 561 82 HOH HOH . I 7 HOH A 62 562 83 HOH HOH . I 7 HOH A 63 563 85 HOH HOH . I 7 HOH A 64 564 86 HOH HOH . I 7 HOH A 65 565 87 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 . . . E 5 14.979 -12.973 -27.746 1 76.03 ? N1 UPG 404 A 1 HETATM 2 C C2 UPG . . . E 5 15.555 -14.112 -27.138 1 75.98 ? C2 UPG 404 A 1 HETATM 3 N N3 UPG . . . E 5 14.778 -14.98 -26.469 1 82.57 ? N3 UPG 404 A 1 HETATM 4 C C4 UPG . . . E 5 13.459 -14.795 -26.364 1 80.45 ? C4 UPG 404 A 1 HETATM 5 C C5 UPG . . . E 5 12.867 -13.684 -26.954 1 67.77 ? C5 UPG 404 A 1 HETATM 6 C C6 UPG . . . E 5 13.655 -12.772 -27.645 1 71.42 ? C6 UPG 404 A 1 HETATM 7 O O2 UPG . . . E 5 16.789 -14.32 -27.213 1 61.14 ? O2 UPG 404 A 1 HETATM 8 O O4 UPG . . . E 5 12.765 -15.623 -25.735 1 77.43 ? O4 UPG 404 A 1 HETATM 9 C C1C UPG . . . E 5 15.817 -12.008 -28.475 1 72.61 ? C1C UPG 404 A 1 HETATM 10 C C2C UPG . . . E 5 15.455 -11.93 -29.951 1 71.46 ? C2C UPG 404 A 1 HETATM 11 O O2C UPG . . . E 5 16.276 -12.814 -30.71 1 78.81 ? O2C UPG 404 A 1 HETATM 12 C C3C UPG . . . E 5 15.706 -10.485 -30.321 1 75.92 ? C3C UPG 404 A 1 HETATM 13 C C4C UPG . . . E 5 15.726 -9.732 -29.002 1 81.29 ? C4C UPG 404 A 1 HETATM 14 O O4C UPG . . . E 5 15.635 -10.695 -27.952 1 72.85 ? O4C UPG 404 A 1 HETATM 15 O O3C UPG . . . E 5 16.957 -10.34 -31.002 1 71.15 ? O3C UPG 404 A 1 HETATM 16 C C5C UPG . . . E 5 14.547 -8.778 -28.888 1 82.19 ? C5C UPG 404 A 1 HETATM 17 O O5C UPG . . . E 5 13.338 -9.541 -28.855 1 75.53 ? O5C UPG 404 A 1 HETATM 18 P PA UPG . . . E 5 12.074 -9.14 -29.766 1 74.51 ? PA UPG 404 A 1 HETATM 19 O O1A UPG . . . E 5 12.506 -8.537 -31.084 1 90.12 ? O1A UPG 404 A 1 HETATM 20 O O2A UPG . . . E 5 11.196 -10.349 -29.991 1 68.1 ? O2A UPG 404 A 1 HETATM 21 O O3A UPG . . . E 5 11.321 -8.075 -28.83 1 73.99 ? O3A UPG 404 A 1 HETATM 22 P PB UPG . . . E 5 10.81 -6.647 -29.361 1 76.85 ? PB UPG 404 A 1 HETATM 23 O O1B UPG . . . E 5 9.422 -6.762 -29.941 1 75.17 ? O1B UPG 404 A 1 HETATM 24 O O2B UPG . . . E 5 11.766 -6.049 -30.366 1 87.48 ? O2B UPG 404 A 1 HETATM 25 O O3B UPG . . . E 5 10.833 -5.862 -27.962 1 91.8 ? O3B UPG 404 A 1 HETATM 26 C C1' UPG . . . E 5 11.471 -4.613 -27.708 1 90.52 ? C1' UPG 404 A 1 HETATM 27 C C2' UPG . . . E 5 12.988 -4.725 -27.753 1 83.95 ? C2' UPG 404 A 1 HETATM 28 C C3' UPG . . . E 5 13.438 -5.838 -26.818 1 78.58 ? C3' UPG 404 A 1 HETATM 29 C C4' UPG . . . E 5 12.897 -5.611 -25.415 1 85.28 ? C4' UPG 404 A 1 HETATM 30 C C5' UPG . . . E 5 11.39 -5.3 -25.436 1 82.16 ? C5' UPG 404 A 1 HETATM 31 C C6' UPG . . . E 5 10.843 -4.948 -24.058 1 71.5 ? C6' UPG 404 A 1 HETATM 32 O O2' UPG . . . E 5 13.435 -4.957 -29.095 1 81.26 ? O2' UPG 404 A 1 HETATM 33 O O3' UPG . . . E 5 14.866 -5.863 -26.761 1 73.68 ? O3' UPG 404 A 1 HETATM 34 O O4' UPG . . . E 5 13.121 -6.791 -24.625 1 94.8 ? O4' UPG 404 A 1 HETATM 35 O O5' UPG . . . E 5 11.096 -4.252 -26.382 1 70.65 ? O5' UPG 404 A 1 HETATM 36 O O6' UPG . . . E 5 11.874 -4.451 -23.205 1 72.78 ? O6' UPG 404 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #