data_4Y6U # _model_server_result.job_id Sm8IE_Cj8fxjMavX2g6gzA _model_server_result.datetime_utc '2024-10-20 00:30:41' _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 4y6u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4Y6U # _exptl.entry_id 4Y6U _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 4Y6U _cell.length_a 99.28 _cell.length_b 99.28 _cell.length_c 128.23 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y6U _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,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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 99.28 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc3 B MN MN . A MN 401 1_555 E O1A UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc4 B MN MN . A MN 401 1_555 E O2B UPG . A UPG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc5 B MN MN . A MN 401 1_555 I O HOH . A HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc6 B MN MN . A MN 401 1_555 I O HOH . A HOH 531 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _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 4Y6U _atom_sites.fract_transf_matrix[1][1] 0.010073 _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] 0.010073 _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] 0.007798 _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 3 EDO EDO . G 6 EDO A 1 406 4 EDO EDO . H 6 EDO A 1 407 5 EDO EDO . I 7 HOH A 1 501 59 HOH HOH . I 7 HOH A 2 502 62 HOH HOH . I 7 HOH A 3 503 46 HOH HOH . I 7 HOH A 4 504 15 HOH HOH . I 7 HOH A 5 505 29 HOH HOH . I 7 HOH A 6 506 65 HOH HOH . I 7 HOH A 7 507 3 HOH HOH . I 7 HOH A 8 508 17 HOH HOH . I 7 HOH A 9 509 82 HOH HOH . I 7 HOH A 10 510 92 HOH HOH . I 7 HOH A 11 511 13 HOH HOH . I 7 HOH A 12 512 30 HOH HOH . I 7 HOH A 13 513 16 HOH HOH . I 7 HOH A 14 514 36 HOH HOH . I 7 HOH A 15 515 26 HOH HOH . I 7 HOH A 16 516 19 HOH HOH . I 7 HOH A 17 517 91 HOH HOH . I 7 HOH A 18 518 20 HOH HOH . I 7 HOH A 19 519 60 HOH HOH . I 7 HOH A 20 520 96 HOH HOH . I 7 HOH A 21 521 31 HOH HOH . I 7 HOH A 22 522 6 HOH HOH . I 7 HOH A 23 523 2 HOH HOH . I 7 HOH A 24 524 21 HOH HOH . I 7 HOH A 25 525 22 HOH HOH . I 7 HOH A 26 526 12 HOH HOH . I 7 HOH A 27 527 44 HOH HOH . I 7 HOH A 28 528 63 HOH HOH . I 7 HOH A 29 529 66 HOH HOH . I 7 HOH A 30 530 94 HOH HOH . I 7 HOH A 31 531 1 HOH HOH . I 7 HOH A 32 532 8 HOH HOH . I 7 HOH A 33 533 18 HOH HOH . I 7 HOH A 34 534 27 HOH HOH . I 7 HOH A 35 535 41 HOH HOH . I 7 HOH A 36 536 58 HOH HOH . I 7 HOH A 37 537 34 HOH HOH . I 7 HOH A 38 538 35 HOH HOH . I 7 HOH A 39 539 85 HOH HOH . I 7 HOH A 40 540 53 HOH HOH . I 7 HOH A 41 541 42 HOH HOH . I 7 HOH A 42 542 32 HOH HOH . I 7 HOH A 43 543 71 HOH HOH . I 7 HOH A 44 544 25 HOH HOH . I 7 HOH A 45 545 57 HOH HOH . I 7 HOH A 46 546 11 HOH HOH . I 7 HOH A 47 547 23 HOH HOH . I 7 HOH A 48 548 39 HOH HOH . I 7 HOH A 49 549 104 HOH HOH . I 7 HOH A 50 550 110 HOH HOH . I 7 HOH A 51 551 52 HOH HOH . I 7 HOH A 52 552 10 HOH HOH . I 7 HOH A 53 553 48 HOH HOH . I 7 HOH A 54 554 4 HOH HOH . I 7 HOH A 55 555 68 HOH HOH . I 7 HOH A 56 556 88 HOH HOH . I 7 HOH A 57 557 45 HOH HOH . I 7 HOH A 58 558 9 HOH HOH . I 7 HOH A 59 559 33 HOH HOH . I 7 HOH A 60 560 79 HOH HOH . I 7 HOH A 61 561 61 HOH HOH . I 7 HOH A 62 562 24 HOH HOH . I 7 HOH A 63 563 14 HOH HOH . I 7 HOH A 64 564 38 HOH HOH . I 7 HOH A 65 565 81 HOH HOH . I 7 HOH A 66 566 7 HOH HOH . I 7 HOH A 67 567 89 HOH HOH . I 7 HOH A 68 568 64 HOH HOH . I 7 HOH A 69 569 5 HOH HOH . I 7 HOH A 70 570 37 HOH HOH . I 7 HOH A 71 571 87 HOH HOH . I 7 HOH A 72 572 43 HOH HOH . I 7 HOH A 73 573 47 HOH HOH . I 7 HOH A 74 574 28 HOH HOH . I 7 HOH A 75 575 74 HOH HOH . I 7 HOH A 76 576 86 HOH HOH . I 7 HOH A 77 577 108 HOH HOH . I 7 HOH A 78 578 111 HOH HOH . I 7 HOH A 79 579 95 HOH HOH . I 7 HOH A 80 580 70 HOH HOH . I 7 HOH A 81 581 109 HOH HOH . I 7 HOH A 82 582 50 HOH HOH . I 7 HOH A 83 583 55 HOH HOH . I 7 HOH A 84 584 51 HOH HOH . I 7 HOH A 85 585 76 HOH HOH . I 7 HOH A 86 586 84 HOH HOH . I 7 HOH A 87 587 80 HOH HOH . I 7 HOH A 88 588 40 HOH HOH . I 7 HOH A 89 589 69 HOH HOH . I 7 HOH A 90 590 107 HOH HOH . I 7 HOH A 91 591 98 HOH HOH . I 7 HOH A 92 592 90 HOH HOH . I 7 HOH A 93 593 106 HOH HOH . I 7 HOH A 94 594 83 HOH HOH . I 7 HOH A 95 595 72 HOH HOH . I 7 HOH A 96 596 49 HOH HOH . I 7 HOH A 97 597 78 HOH HOH . I 7 HOH A 98 598 73 HOH HOH . I 7 HOH A 99 599 67 HOH HOH . I 7 HOH A 100 600 56 HOH HOH . I 7 HOH A 101 601 77 HOH HOH . I 7 HOH A 102 602 93 HOH HOH . I 7 HOH A 103 603 75 HOH HOH . I 7 HOH A 104 604 97 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 34.642 -13.168 27.279 1 38.99 ? N1 UPG 404 A 1 HETATM 2 C C2 UPG . . . E 5 33.985 -14.224 26.611 1 51.16 ? C2 UPG 404 A 1 HETATM 3 N N3 UPG . . . E 5 34.704 -15.093 25.853 1 49.81 ? N3 UPG 404 A 1 HETATM 4 C C4 UPG . . . E 5 36.042 -14.965 25.733 1 52.39 ? C4 UPG 404 A 1 HETATM 5 C C5 UPG . . . E 5 36.711 -13.913 26.37 1 44.96 ? C5 UPG 404 A 1 HETATM 6 C C6 UPG . . . E 5 35.977 -13.004 27.125 1 44.82 ? C6 UPG 404 A 1 HETATM 7 O O2 UPG . . . E 5 32.746 -14.345 26.745 1 41.38 ? O2 UPG 404 A 1 HETATM 8 O O4 UPG . . . E 5 36.693 -15.794 25.054 1 48.67 ? O4 UPG 404 A 1 HETATM 9 C C1C UPG . . . E 5 33.867 -12.189 28.029 1 42.58 ? C1C UPG 404 A 1 HETATM 10 C C2C UPG . . . E 5 34.358 -11.977 29.461 1 42.59 ? C2C UPG 404 A 1 HETATM 11 O O2C UPG . . . E 5 33.729 -12.947 30.272 1 39.13 ? O2C UPG 404 A 1 HETATM 12 C C3C UPG . . . E 5 33.914 -10.573 29.733 1 43.86 ? C3C UPG 404 A 1 HETATM 13 C C4C UPG . . . E 5 33.919 -9.886 28.359 1 44.47 ? C4C UPG 404 A 1 HETATM 14 O O4C UPG . . . E 5 33.982 -10.923 27.38 1 44.92 ? O4C UPG 404 A 1 HETATM 15 O O3C UPG . . . E 5 32.613 -10.626 30.305 1 39.05 ? O3C UPG 404 A 1 HETATM 16 C C5C UPG . . . E 5 35.117 -8.95 28.242 1 41.73 ? C5C UPG 404 A 1 HETATM 17 O O5C UPG . . . E 5 36.276 -9.757 28.392 1 41.21 ? O5C UPG 404 A 1 HETATM 18 P PA UPG . . . E 5 37.527 -9.275 29.271 1 44.27 ? PA UPG 404 A 1 HETATM 19 O O1A UPG . . . E 5 37.051 -8.794 30.654 1 50.43 ? O1A UPG 404 A 1 HETATM 20 O O2A UPG . . . E 5 38.391 -10.509 29.455 1 37.01 ? O2A UPG 404 A 1 HETATM 21 O O3A UPG . . . E 5 38.152 -8.091 28.362 1 52.61 ? O3A UPG 404 A 1 HETATM 22 P PB UPG . . . E 5 38.842 -6.678 28.804 1 47.86 ? PB UPG 404 A 1 HETATM 23 O O1B UPG . . . E 5 40.229 -6.952 29.274 1 49.51 ? O1B UPG 404 A 1 HETATM 24 O O2B UPG . . . E 5 37.977 -5.863 29.734 1 49.33 ? O2B UPG 404 A 1 HETATM 25 O O3B UPG . . . E 5 38.886 -5.909 27.398 1 46.69 ? O3B UPG 404 A 1 HETATM 26 C C1' UPG . . . E 5 38.266 -4.665 27.035 1 51.37 ? C1' UPG 404 A 1 HETATM 27 C C2' UPG . . . E 5 36.728 -4.688 27.076 1 52.46 ? C2' UPG 404 A 1 HETATM 28 C C3' UPG . . . E 5 36.21 -5.892 26.304 1 48.9 ? C3' UPG 404 A 1 HETATM 29 C C4' UPG . . . E 5 36.715 -5.787 24.88 1 46.85 ? C4' UPG 404 A 1 HETATM 30 C C5' UPG . . . E 5 38.217 -5.594 24.835 1 42.3 ? C5' UPG 404 A 1 HETATM 31 C C6' UPG . . . E 5 38.655 -5.46 23.365 1 41.81 ? C6' UPG 404 A 1 HETATM 32 O O2' UPG . . . E 5 36.222 -4.73 28.421 1 49.34 ? O2' UPG 404 A 1 HETATM 33 O O3' UPG . . . E 5 34.77 -5.954 26.37 1 39.51 ? O3' UPG 404 A 1 HETATM 34 O O4' UPG . . . E 5 36.408 -6.958 24.105 1 51.55 ? O4' UPG 404 A 1 HETATM 35 O O5' UPG . . . E 5 38.599 -4.476 25.659 1 52.91 ? O5' UPG 404 A 1 HETATM 36 O O6' UPG . . . E 5 37.7 -4.676 22.647 1 42.89 ? O6' UPG 404 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #