data_7Z5Y # _model_server_result.job_id VSosHKZwt_ugcIU1orUm5w _model_server_result.datetime_utc '2024-11-27 23:54:26' _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 7z5y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 7Z5Y # _exptl.entry_id 7Z5Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 102.78 _cell.angle_gamma 90 _cell.entry_id 7Z5Y _cell.length_a 42.16 _cell.length_b 101.96 _cell.length_c 46.19 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z5Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 covale ? covale1 E PB UDP . A UDP 402 1_555 F O1 MUB . C MUB 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.553 ? covale ? covale2 B O3' 6HA 1 B 6HA 7 1_555 B P 6HC 2 B 6HC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.559 ? covale ? covale3 B O3' 6HC 2 B 6HC 8 1_555 B P 6HC 3 B 6HC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.56 ? covale ? covale4 B O3' 6HC 3 B 6HC 9 1_555 B P A9Z 4 B A9Z 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.56 ? covale ? covale5 B C7T A9Z 4 B A9Z 10 1_555 C SG CYS 3 C CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale6 C C ALA 1 C ALA 3 1_555 C N FGA 2 C FGA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 C N ALA 1 C ALA 3 1_555 F C10 MUB . C MUB 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 C CD FGA 2 C FGA 4 1_555 C N CYS 3 C CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale9 C C CYS 3 C CYS 5 1_555 C N DAL 4 C DAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 C C DAL 4 C DAL 6 1_555 C N DAL 5 C DAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 UDP sing 570 n n N1 C6 UDP sing 571 n n N1 C1' UDP sing 572 n n C2 N3 UDP sing 573 n n C2 O2 UDP doub 574 n n N3 C4 UDP sing 575 n n N3 HN3 UDP sing 576 n n C4 C5 UDP sing 577 n n C4 O4 UDP doub 578 n n C5 C6 UDP doub 579 n n C5 H5 UDP sing 580 n n C6 H6 UDP sing 581 n n C1' C2' UDP sing 582 n n C1' O4' UDP sing 583 n n C1' H1' UDP sing 584 n n C2' O2' UDP sing 585 n n C2' C3' UDP sing 586 n n C2' H2' UDP sing 587 n n O2' HO2' UDP sing 588 n n C3' C4' UDP sing 589 n n C3' O3' UDP sing 590 n n C3' H3' UDP sing 591 n n C4' O4' UDP sing 592 n n C4' C5' UDP sing 593 n n C4' H4' UDP sing 594 n n O3' HO3' UDP sing 595 n n C5' O5' UDP sing 596 n n C5' "H5'1" UDP sing 597 n n C5' "H5'2" UDP sing 598 n n O5' PA UDP sing 599 n n PA O1A UDP doub 600 n n PA O2A UDP sing 601 n n PA O3A UDP sing 602 n n O2A HOA2 UDP sing 603 n n O3A PB UDP sing 604 n n PB O1B UDP doub 605 n n PB O2B UDP sing 606 n n PB O3B UDP sing 607 n n O2B HOB2 UDP sing 608 n n O3B HOB3 UDP sing 609 n n # _atom_sites.entry_id 7Z5Y _atom_sites.fract_transf_matrix[1][1] 0.023719 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00538 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009808 _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] 0.0222 _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 D 4 GOL A 1 401 401 GOL GOL . E 5 UDP A 1 402 1 UDP UDP . F 6 MUB C 1 101 2 MUB MUB . G 7 HOH A 1 501 82 HOH HOH . G 7 HOH A 2 502 129 HOH HOH . G 7 HOH A 3 503 79 HOH HOH . G 7 HOH A 4 504 23 HOH HOH . G 7 HOH A 5 505 130 HOH HOH . G 7 HOH A 6 506 120 HOH HOH . G 7 HOH A 7 507 105 HOH HOH . G 7 HOH A 8 508 50 HOH HOH . G 7 HOH A 9 509 101 HOH HOH . G 7 HOH A 10 510 68 HOH HOH . G 7 HOH A 11 511 60 HOH HOH . G 7 HOH A 12 512 126 HOH HOH . G 7 HOH A 13 513 38 HOH HOH . G 7 HOH A 14 514 128 HOH HOH . G 7 HOH A 15 515 59 HOH HOH . G 7 HOH A 16 516 28 HOH HOH . G 7 HOH A 17 517 134 HOH HOH . G 7 HOH A 18 518 49 HOH HOH . G 7 HOH A 19 519 39 HOH HOH . G 7 HOH A 20 520 41 HOH HOH . G 7 HOH A 21 521 9 HOH HOH . G 7 HOH A 22 522 75 HOH HOH . G 7 HOH A 23 523 46 HOH HOH . G 7 HOH A 24 524 77 HOH HOH . G 7 HOH A 25 525 20 HOH HOH . G 7 HOH A 26 526 57 HOH HOH . G 7 HOH A 27 527 84 HOH HOH . G 7 HOH A 28 528 4 HOH HOH . G 7 HOH A 29 529 52 HOH HOH . G 7 HOH A 30 530 24 HOH HOH . G 7 HOH A 31 531 61 HOH HOH . G 7 HOH A 32 532 69 HOH HOH . G 7 HOH A 33 533 93 HOH HOH . G 7 HOH A 34 534 89 HOH HOH . G 7 HOH A 35 535 83 HOH HOH . G 7 HOH A 36 536 78 HOH HOH . G 7 HOH A 37 537 65 HOH HOH . G 7 HOH A 38 538 10 HOH HOH . G 7 HOH A 39 539 53 HOH HOH . G 7 HOH A 40 540 122 HOH HOH . G 7 HOH A 41 541 54 HOH HOH . G 7 HOH A 42 542 62 HOH HOH . G 7 HOH A 43 543 131 HOH HOH . G 7 HOH A 44 544 48 HOH HOH . G 7 HOH A 45 545 18 HOH HOH . G 7 HOH A 46 546 72 HOH HOH . G 7 HOH A 47 547 11 HOH HOH . G 7 HOH A 48 548 15 HOH HOH . G 7 HOH A 49 549 88 HOH HOH . G 7 HOH A 50 550 114 HOH HOH . G 7 HOH A 51 551 51 HOH HOH . G 7 HOH A 52 552 47 HOH HOH . G 7 HOH A 53 553 22 HOH HOH . G 7 HOH A 54 554 74 HOH HOH . G 7 HOH A 55 555 31 HOH HOH . G 7 HOH A 56 556 100 HOH HOH . G 7 HOH A 57 557 112 HOH HOH . G 7 HOH A 58 558 29 HOH HOH . G 7 HOH A 59 559 91 HOH HOH . G 7 HOH A 60 560 25 HOH HOH . G 7 HOH A 61 561 76 HOH HOH . G 7 HOH A 62 562 102 HOH HOH . G 7 HOH A 63 563 45 HOH HOH . G 7 HOH A 64 564 66 HOH HOH . G 7 HOH A 65 565 2 HOH HOH . G 7 HOH A 66 566 73 HOH HOH . G 7 HOH A 67 567 43 HOH HOH . G 7 HOH A 68 568 67 HOH HOH . G 7 HOH A 69 569 35 HOH HOH . G 7 HOH A 70 570 8 HOH HOH . G 7 HOH A 71 571 86 HOH HOH . G 7 HOH A 72 572 135 HOH HOH . G 7 HOH A 73 573 110 HOH HOH . G 7 HOH A 74 574 107 HOH HOH . G 7 HOH A 75 575 103 HOH HOH . G 7 HOH A 76 576 124 HOH HOH . G 7 HOH A 77 577 19 HOH HOH . G 7 HOH A 78 578 13 HOH HOH . G 7 HOH A 79 579 6 HOH HOH . G 7 HOH A 80 580 42 HOH HOH . G 7 HOH A 81 581 125 HOH HOH . G 7 HOH A 82 582 36 HOH HOH . G 7 HOH A 83 583 58 HOH HOH . G 7 HOH A 84 584 97 HOH HOH . G 7 HOH A 85 585 70 HOH HOH . G 7 HOH A 86 586 33 HOH HOH . G 7 HOH A 87 587 117 HOH HOH . G 7 HOH A 88 588 94 HOH HOH . G 7 HOH A 89 589 133 HOH HOH . G 7 HOH A 90 590 32 HOH HOH . G 7 HOH A 91 591 113 HOH HOH . G 7 HOH A 92 592 64 HOH HOH . G 7 HOH A 93 593 115 HOH HOH . G 7 HOH A 94 594 71 HOH HOH . G 7 HOH A 95 595 111 HOH HOH . G 7 HOH A 96 596 118 HOH HOH . G 7 HOH A 97 597 12 HOH HOH . G 7 HOH A 98 598 95 HOH HOH . G 7 HOH A 99 599 87 HOH HOH . G 7 HOH A 100 600 90 HOH HOH . G 7 HOH A 101 601 7 HOH HOH . G 7 HOH A 102 602 132 HOH HOH . G 7 HOH A 103 603 34 HOH HOH . G 7 HOH A 104 604 99 HOH HOH . G 7 HOH A 105 605 5 HOH HOH . G 7 HOH A 106 606 26 HOH HOH . G 7 HOH A 107 607 14 HOH HOH . G 7 HOH A 108 608 55 HOH HOH . G 7 HOH A 109 609 127 HOH HOH . G 7 HOH A 110 610 104 HOH HOH . G 7 HOH A 111 611 106 HOH HOH . G 7 HOH A 112 612 44 HOH HOH . G 7 HOH A 113 613 17 HOH HOH . G 7 HOH A 114 614 37 HOH HOH . G 7 HOH A 115 615 80 HOH HOH . G 7 HOH A 116 616 63 HOH HOH . G 7 HOH A 117 617 119 HOH HOH . G 7 HOH A 118 618 98 HOH HOH . G 7 HOH A 119 619 3 HOH HOH . G 7 HOH A 120 620 30 HOH HOH . G 7 HOH A 121 621 1 HOH HOH . G 7 HOH A 122 622 85 HOH HOH . G 7 HOH A 123 623 96 HOH HOH . G 7 HOH A 124 624 27 HOH HOH . G 7 HOH A 125 625 108 HOH HOH . G 7 HOH A 126 626 81 HOH HOH . G 7 HOH A 127 627 92 HOH HOH . G 7 HOH A 128 628 21 HOH HOH . G 7 HOH A 129 629 40 HOH HOH . H 7 HOH B 1 101 109 HOH HOH . H 7 HOH B 2 102 116 HOH HOH . I 7 HOH C 1 201 16 HOH HOH . I 7 HOH C 2 202 56 HOH HOH . I 7 HOH C 3 203 121 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 UDP . . . E 5 6.869 -14.769 19.175 1 28.31 ? N1 UDP 402 A 1 HETATM 2 C C2 UDP . . . E 5 5.769 -15.204 19.913 1 32.99 ? C2 UDP 402 A 1 HETATM 3 N N3 UDP . . . E 5 5.486 -16.547 19.79 1 28.15 ? N3 UDP 402 A 1 HETATM 4 C C4 UDP . . . E 5 6.166 -17.474 19.017 1 27.76 ? C4 UDP 402 A 1 HETATM 5 C C5 UDP . . . E 5 7.288 -16.947 18.293 1 25.65 ? C5 UDP 402 A 1 HETATM 6 C C6 UDP . . . E 5 7.592 -15.635 18.387 1 25.55 ? C6 UDP 402 A 1 HETATM 7 O O2 UDP . . . E 5 5.091 -14.455 20.613 1 29.44 ? O2 UDP 402 A 1 HETATM 8 O O4 UDP . . . E 5 5.785 -18.663 19.002 1 26.56 ? O4 UDP 402 A 1 HETATM 9 C C1' UDP . . . E 5 7.256 -13.354 19.291 1 29.9 ? C1' UDP 402 A 1 HETATM 10 C C2' UDP . . . E 5 8.751 -13.15 19.529 1 32.36 ? C2' UDP 402 A 1 HETATM 11 O O2' UDP . . . E 5 9.105 -13.399 20.885 1 34.18 ? O2' UDP 402 A 1 HETATM 12 C C3' UDP . . . E 5 8.893 -11.676 19.141 1 32.63 ? C3' UDP 402 A 1 HETATM 13 C C4' UDP . . . E 5 7.825 -11.501 18.056 1 30.71 ? C4' UDP 402 A 1 HETATM 14 O O4' UDP . . . E 5 7.01 -12.699 18.072 1 29.21 ? O4' UDP 402 A 1 HETATM 15 O O3' UDP . . . E 5 8.558 -10.82 20.224 1 35.83 ? O3' UDP 402 A 1 HETATM 16 C C5' UDP . . . E 5 8.376 -11.257 16.679 1 31.58 ? C5' UDP 402 A 1 HETATM 17 O O5' UDP . . . E 5 8.987 -9.953 16.721 1 31.84 ? O5' UDP 402 A 1 HETATM 18 P PA UDP . . . E 5 9.302 -9.165 15.402 1 27.18 ? PA UDP 402 A 1 HETATM 19 O O1A UDP . . . E 5 8.025 -9.011 14.668 1 28.07 ? O1A UDP 402 A 1 HETATM 20 O O2A UDP . . . E 5 10.084 -7.888 15.707 1 33.67 ? O2A UDP 402 A 1 HETATM 21 O O3A UDP . . . E 5 10.298 -10.14 14.587 1 29.38 ? O3A UDP 402 A 1 HETATM 22 P PB UDP . . . E 5 11.715 -9.849 13.934 1 26.62 ? PB UDP 402 A 1 HETATM 23 O O1B UDP . . . E 5 11.414 -8.76 12.906 1 23.76 ? O1B UDP 402 A 1 HETATM 24 O O3B UDP . . . E 5 12.016 -11.136 13.169 1 24.59 ? O3B UDP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #