data_1ZDG # _model_server_result.job_id FP2rjpIGpIH6RKl1gLEtAA _model_server_result.datetime_utc '2024-10-25 20:21:12' _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 1zdg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":411}' # _entry.id 1ZDG # _exptl.entry_id 1ZDG _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 1ZDG _cell.length_a 57.6 _cell.length_b 106.69 _cell.length_c 123.49 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -106.69 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 122 A ASP 101 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A OD1 ASP 124 A ASP 103 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc3 A OD2 ASP 124 A ASP 103 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc4 A NE2 HIS 232 A HIS 211 1_555 B MN MN . A MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc5 B MN MN . A MN 400 1_555 D O1A UPG . A UPG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc6 B MN MN . A MN 400 1_555 D O1B UPG . A UPG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? # _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 362 n n N1 C6 UPG sing 363 n n N1 C1C UPG sing 364 n n C2 N3 UPG sing 365 n n C2 O2 UPG doub 366 n n N3 C4 UPG sing 367 n n N3 HN3 UPG sing 368 n n C4 C5 UPG sing 369 n n C4 O4 UPG doub 370 n n C5 C6 UPG doub 371 n n C5 H5 UPG sing 372 n n C6 H6 UPG sing 373 n n C1C C2C UPG sing 374 n n C1C O4C UPG sing 375 n n C1C H1C UPG sing 376 n n C2C O2C UPG sing 377 n n C2C C3C UPG sing 378 n n C2C H2C UPG sing 379 n n O2C HO2C UPG sing 380 n n C3C C4C UPG sing 381 n n C3C O3C UPG sing 382 n n C3C H3C UPG sing 383 n n C4C O4C UPG sing 384 n n C4C C5C UPG sing 385 n n C4C H4C UPG sing 386 n n O3C HO3C UPG sing 387 n n C5C O5C UPG sing 388 n n C5C H5C1 UPG sing 389 n n C5C H5C2 UPG sing 390 n n O5C PA UPG sing 391 n n PA O1A UPG doub 392 n n PA O2A UPG sing 393 n n PA O3A UPG sing 394 n n O2A HOA2 UPG sing 395 n n O3A PB UPG sing 396 n n PB O1B UPG doub 397 n n PB O2B UPG sing 398 n n PB O3B UPG sing 399 n n O2B HOB2 UPG sing 400 n n O3B C1' UPG sing 401 n n C1' C2' UPG sing 402 n n C1' O5' UPG sing 403 n n C1' H1' UPG sing 404 n n C2' C3' UPG sing 405 n n C2' O2' UPG sing 406 n n C2' H2' UPG sing 407 n n C3' C4' UPG sing 408 n n C3' O3' UPG sing 409 n n C3' H3' UPG sing 410 n n C4' C5' UPG sing 411 n n C4' O4' UPG sing 412 n n C4' H4' UPG sing 413 n n C5' C6' UPG sing 414 n n C5' O5' UPG sing 415 n n C5' H5' UPG sing 416 n n C6' O6' UPG sing 417 n n C6' "H6'1" UPG sing 418 n n C6' "H6'2" UPG sing 419 n n O2' HO2' UPG sing 420 n n O3' HO3' UPG sing 421 n n O4' HO4' UPG sing 422 n n O6' HO6' UPG sing 423 n n # _atom_sites.entry_id 1ZDG _atom_sites.fract_transf_matrix[1][1] 0.017361 _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] 0.009373 _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] 0.008098 _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 1 400 400 MN MN . C 3 SO4 A 1 401 401 SO4 SO4 . D 4 UPG A 1 411 411 UPG UPG . E 5 HOH A 1 412 1 HOH WAT . E 5 HOH A 2 413 2 HOH WAT . E 5 HOH A 3 414 3 HOH WAT . E 5 HOH A 4 415 4 HOH WAT . E 5 HOH A 5 416 5 HOH WAT . E 5 HOH A 6 417 6 HOH WAT . E 5 HOH A 7 418 7 HOH WAT . E 5 HOH A 8 419 8 HOH WAT . E 5 HOH A 9 420 9 HOH WAT . E 5 HOH A 10 421 10 HOH WAT . E 5 HOH A 11 422 11 HOH WAT . E 5 HOH A 12 423 12 HOH WAT . E 5 HOH A 13 424 13 HOH WAT . E 5 HOH A 14 425 14 HOH WAT . E 5 HOH A 15 426 15 HOH WAT . E 5 HOH A 16 427 16 HOH WAT . E 5 HOH A 17 428 17 HOH WAT . E 5 HOH A 18 429 18 HOH WAT . E 5 HOH A 19 430 19 HOH WAT . E 5 HOH A 20 431 20 HOH WAT . E 5 HOH A 21 432 21 HOH WAT . E 5 HOH A 22 433 22 HOH WAT . E 5 HOH A 23 434 23 HOH WAT . E 5 HOH A 24 435 24 HOH WAT . E 5 HOH A 25 436 25 HOH WAT . E 5 HOH A 26 437 26 HOH WAT . E 5 HOH A 27 438 27 HOH WAT . E 5 HOH A 28 439 28 HOH WAT . E 5 HOH A 29 440 30 HOH WAT . E 5 HOH A 30 441 31 HOH WAT . E 5 HOH A 31 442 32 HOH WAT . E 5 HOH A 32 443 33 HOH WAT . E 5 HOH A 33 444 34 HOH WAT . E 5 HOH A 34 445 35 HOH WAT . E 5 HOH A 35 446 36 HOH WAT . E 5 HOH A 36 447 37 HOH WAT . E 5 HOH A 37 448 38 HOH WAT . E 5 HOH A 38 449 39 HOH WAT . E 5 HOH A 39 450 40 HOH WAT . E 5 HOH A 40 451 41 HOH WAT . E 5 HOH A 41 452 42 HOH WAT . E 5 HOH A 42 453 44 HOH WAT . E 5 HOH A 43 454 45 HOH WAT . E 5 HOH A 44 455 46 HOH WAT . E 5 HOH A 45 456 48 HOH WAT . E 5 HOH A 46 457 49 HOH WAT . E 5 HOH A 47 458 50 HOH WAT . E 5 HOH A 48 459 51 HOH WAT . E 5 HOH A 49 460 52 HOH WAT . E 5 HOH A 50 461 53 HOH WAT . E 5 HOH A 51 462 54 HOH WAT . E 5 HOH A 52 463 55 HOH WAT . E 5 HOH A 53 464 56 HOH WAT . E 5 HOH A 54 465 57 HOH WAT . E 5 HOH A 55 466 58 HOH WAT . E 5 HOH A 56 467 59 HOH WAT . E 5 HOH A 57 468 60 HOH WAT . E 5 HOH A 58 469 61 HOH WAT . E 5 HOH A 59 470 62 HOH WAT . E 5 HOH A 60 471 63 HOH WAT . E 5 HOH A 61 472 64 HOH WAT . E 5 HOH A 62 473 65 HOH WAT . E 5 HOH A 63 474 66 HOH WAT . E 5 HOH A 64 475 67 HOH WAT . E 5 HOH A 65 476 68 HOH WAT . E 5 HOH A 66 477 69 HOH WAT . E 5 HOH A 67 478 70 HOH WAT . E 5 HOH A 68 479 71 HOH WAT . E 5 HOH A 69 480 72 HOH WAT . E 5 HOH A 70 481 73 HOH WAT . E 5 HOH A 71 482 74 HOH WAT . E 5 HOH A 72 483 75 HOH WAT . E 5 HOH A 73 484 76 HOH WAT . E 5 HOH A 74 485 77 HOH WAT . E 5 HOH A 75 486 78 HOH WAT . E 5 HOH A 76 487 79 HOH WAT . E 5 HOH A 77 488 80 HOH WAT . E 5 HOH A 78 489 81 HOH WAT . E 5 HOH A 79 490 82 HOH WAT . E 5 HOH A 80 491 83 HOH WAT . E 5 HOH A 81 492 84 HOH WAT . E 5 HOH A 82 493 85 HOH WAT . E 5 HOH A 83 494 86 HOH WAT . E 5 HOH A 84 495 87 HOH WAT . E 5 HOH A 85 496 88 HOH WAT . E 5 HOH A 86 497 89 HOH WAT . # 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 7.074 -32.663 87.066 1 55.27 ? N1 UPG 411 A 1 HETATM 2 C C2 UPG . . . D 4 7.683 -31.455 87.41 1 54.98 ? C2 UPG 411 A 1 HETATM 3 N N3 UPG . . . D 4 7.355 -30.93 88.65 1 56.88 ? N3 UPG 411 A 1 HETATM 4 C C4 UPG . . . D 4 6.465 -31.509 89.609 1 59.9 ? C4 UPG 411 A 1 HETATM 5 C C5 UPG . . . D 4 5.852 -32.784 89.201 1 58.12 ? C5 UPG 411 A 1 HETATM 6 C C6 UPG . . . D 4 6.171 -33.304 87.981 1 54.99 ? C6 UPG 411 A 1 HETATM 7 O O2 UPG . . . D 4 8.456 -30.887 86.652 1 51.77 ? O2 UPG 411 A 1 HETATM 8 O O4 UPG . . . D 4 6.277 -30.903 90.681 1 58.05 ? O4 UPG 411 A 1 HETATM 9 C C1C UPG . . . D 4 7.399 -33.261 85.736 1 49.73 ? C1C UPG 411 A 1 HETATM 10 C C2C UPG . . . D 4 8.619 -34.202 85.734 1 48.22 ? C2C UPG 411 A 1 HETATM 11 O O2C UPG . . . D 4 9.306 -34.094 84.494 1 46.26 ? O2C UPG 411 A 1 HETATM 12 C C3C UPG . . . D 4 7.968 -35.542 85.998 1 45.94 ? C3C UPG 411 A 1 HETATM 13 C C4C UPG . . . D 4 6.732 -35.433 85.088 1 47.62 ? C4C UPG 411 A 1 HETATM 14 O O4C UPG . . . D 4 6.299 -34.047 85.315 1 49.81 ? O4C UPG 411 A 1 HETATM 15 O O3C UPG . . . D 4 8.866 -36.558 85.588 1 45.26 ? O3C UPG 411 A 1 HETATM 16 C C5C UPG . . . D 4 5.532 -36.32 85.485 1 48.33 ? C5C UPG 411 A 1 HETATM 17 O O5C UPG . . . D 4 5.445 -36.503 86.917 1 52.11 ? O5C UPG 411 A 1 HETATM 18 P PA UPG . . . D 4 6.071 -37.599 87.874 1 52.34 ? PA UPG 411 A 1 HETATM 19 O O1A UPG . . . D 4 7.329 -38.085 87.242 1 51.32 ? O1A UPG 411 A 1 HETATM 20 O O2A UPG . . . D 4 6.245 -36.99 89.208 1 53.67 ? O2A UPG 411 A 1 HETATM 21 O O3A UPG . . . D 4 4.907 -38.651 87.828 1 53.85 ? O3A UPG 411 A 1 HETATM 22 P PB UPG . . . D 4 4.78 -40.238 87.644 1 50.81 ? PB UPG 411 A 1 HETATM 23 O O1B UPG . . . D 4 5.869 -40.583 86.542 1 50.83 ? O1B UPG 411 A 1 HETATM 24 O O2B UPG . . . D 4 5.199 -40.981 88.821 1 50.79 ? O2B UPG 411 A 1 HETATM 25 O O3B UPG . . . D 4 3.382 -40.274 87.175 1 54.52 ? O3B UPG 411 A 1 HETATM 26 C C1' UPG . . . D 4 2.6 -39.653 86.644 0.75 55.62 ? C1' UPG 411 A 1 HETATM 27 C C2' UPG . . . D 4 1.138 -40.087 86.637 0.75 56.36 ? C2' UPG 411 A 1 HETATM 28 C C3' UPG . . . D 4 0.987 -41.468 86.003 0.75 56.18 ? C3' UPG 411 A 1 HETATM 29 C C4' UPG . . . D 4 1.598 -41.543 84.588 0.75 54.95 ? C4' UPG 411 A 1 HETATM 30 C C5' UPG . . . D 4 3.015 -40.911 84.623 0.75 54.31 ? C5' UPG 411 A 1 HETATM 31 C C6' UPG . . . D 4 3.667 -40.718 83.251 0.75 50.35 ? C6' UPG 411 A 1 HETATM 32 O O2' UPG . . . D 4 0.549 -40.203 87.958 0.75 57.5 ? O2' UPG 411 A 1 HETATM 33 O O3' UPG . . . D 4 -0.418 -41.86 85.953 0.75 58.09 ? O3' UPG 411 A 1 HETATM 34 O O4' UPG . . . D 4 1.707 -42.914 84.158 0.75 57.43 ? O4' UPG 411 A 1 HETATM 35 O O5' UPG . . . D 4 2.986 -39.588 85.284 0.75 55.66 ? O5' UPG 411 A 1 HETATM 36 O O6' UPG . . . D 4 4.112 -39.347 83.074 0.75 48.34 ? O6' UPG 411 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #