data_5F85 # _model_server_result.job_id Taa82jkMUsPGtQocL36czA _model_server_result.datetime_utc '2024-12-26 12:06:52' _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 5f85 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5F85 # _exptl.entry_id 5F85 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 90 _cell.angle_gamma 120 _cell.entry_id 5F85 _cell.length_a 269.829 _cell.length_b 269.829 _cell.length_c 47.28 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F85 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,J,K _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 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 52 A CYS 64 1_555 A SG CYS 63 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 61 A CYS 73 1_555 A SG CYS 366 A CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 108 A CYS 120 1_555 A SG CYS 114 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 270 A CYS 282 1_555 A SG CYS 293 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf5 B SG CYS 9 B CYS 51 1_555 B SG CYS 20 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf6 B SG CYS 14 B CYS 56 1_555 B SG CYS 29 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 31 B CYS 73 1_555 B SG CYS 40 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? # _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 375 n n N1 C6 UDP sing 376 n n N1 C1' UDP sing 377 n n C2 N3 UDP sing 378 n n C2 O2 UDP doub 379 n n N3 C4 UDP sing 380 n n N3 HN3 UDP sing 381 n n C4 C5 UDP sing 382 n n C4 O4 UDP doub 383 n n C5 C6 UDP doub 384 n n C5 H5 UDP sing 385 n n C6 H6 UDP sing 386 n n C1' C2' UDP sing 387 n n C1' O4' UDP sing 388 n n C1' H1' UDP sing 389 n n C2' O2' UDP sing 390 n n C2' C3' UDP sing 391 n n C2' H2' UDP sing 392 n n O2' HO2' UDP sing 393 n n C3' C4' UDP sing 394 n n C3' O3' UDP sing 395 n n C3' H3' UDP sing 396 n n C4' O4' UDP sing 397 n n C4' C5' UDP sing 398 n n C4' H4' UDP sing 399 n n O3' HO3' UDP sing 400 n n C5' O5' UDP sing 401 n n C5' "H5'1" UDP sing 402 n n C5' "H5'2" UDP sing 403 n n O5' PA UDP sing 404 n n PA O1A UDP doub 405 n n PA O2A UDP sing 406 n n PA O3A UDP sing 407 n n O2A HOA2 UDP sing 408 n n O3A PB UDP sing 409 n n PB O1B UDP doub 410 n n PB O2B UDP sing 411 n n PB O3B UDP sing 412 n n O2B HOB2 UDP sing 413 n n O3B HOB3 UDP sing 414 n n # _atom_sites.entry_id 5F85 _atom_sites.fract_transf_matrix[1][1] 0.003706 _atom_sites.fract_transf_matrix[1][2] 0.00214 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004279 _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] 0.021151 _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 C 3 UDP A 1 501 1 UDP UDP . D 4 GOL A 1 502 1 GOL GOL . E 5 SO4 A 1 503 1 SO4 SO4 . F 5 SO4 A 1 504 2 SO4 SO4 . G 5 SO4 A 1 505 3 SO4 SO4 . H 5 SO4 A 1 506 4 SO4 SO4 . I 5 SO4 A 1 507 5 SO4 SO4 . J 6 HOH A 1 601 3 HOH HOH . J 6 HOH A 2 602 107 HOH HOH . J 6 HOH A 3 603 17 HOH HOH . J 6 HOH A 4 604 103 HOH HOH . J 6 HOH A 5 605 81 HOH HOH . J 6 HOH A 6 606 122 HOH HOH . J 6 HOH A 7 607 13 HOH HOH . J 6 HOH A 8 608 8 HOH HOH . J 6 HOH A 9 609 12 HOH HOH . J 6 HOH A 10 610 34 HOH HOH . J 6 HOH A 11 611 58 HOH HOH . J 6 HOH A 12 612 90 HOH HOH . J 6 HOH A 13 613 22 HOH HOH . J 6 HOH A 14 614 44 HOH HOH . J 6 HOH A 15 615 70 HOH HOH . J 6 HOH A 16 616 25 HOH HOH . J 6 HOH A 17 617 109 HOH HOH . J 6 HOH A 18 618 6 HOH HOH . J 6 HOH A 19 619 38 HOH HOH . J 6 HOH A 20 620 15 HOH HOH . J 6 HOH A 21 621 93 HOH HOH . J 6 HOH A 22 622 20 HOH HOH . J 6 HOH A 23 623 79 HOH HOH . J 6 HOH A 24 624 26 HOH HOH . J 6 HOH A 25 625 14 HOH HOH . J 6 HOH A 26 626 101 HOH HOH . J 6 HOH A 27 627 53 HOH HOH . J 6 HOH A 28 628 9 HOH HOH . J 6 HOH A 29 629 78 HOH HOH . J 6 HOH A 30 630 80 HOH HOH . J 6 HOH A 31 631 52 HOH HOH . J 6 HOH A 32 632 28 HOH HOH . J 6 HOH A 33 633 48 HOH HOH . J 6 HOH A 34 634 120 HOH HOH . J 6 HOH A 35 635 66 HOH HOH . J 6 HOH A 36 636 94 HOH HOH . J 6 HOH A 37 637 29 HOH HOH . J 6 HOH A 38 638 121 HOH HOH . J 6 HOH A 39 639 16 HOH HOH . J 6 HOH A 40 640 37 HOH HOH . J 6 HOH A 41 641 18 HOH HOH . J 6 HOH A 42 642 39 HOH HOH . J 6 HOH A 43 643 30 HOH HOH . J 6 HOH A 44 644 87 HOH HOH . J 6 HOH A 45 645 57 HOH HOH . J 6 HOH A 46 646 92 HOH HOH . J 6 HOH A 47 647 4 HOH HOH . J 6 HOH A 48 648 41 HOH HOH . J 6 HOH A 49 649 43 HOH HOH . J 6 HOH A 50 650 68 HOH HOH . J 6 HOH A 51 651 67 HOH HOH . J 6 HOH A 52 652 76 HOH HOH . J 6 HOH A 53 653 11 HOH HOH . J 6 HOH A 54 654 105 HOH HOH . J 6 HOH A 55 655 24 HOH HOH . J 6 HOH A 56 656 64 HOH HOH . J 6 HOH A 57 657 91 HOH HOH . J 6 HOH A 58 658 97 HOH HOH . J 6 HOH A 59 659 100 HOH HOH . J 6 HOH A 60 660 59 HOH HOH . J 6 HOH A 61 661 115 HOH HOH . J 6 HOH A 62 662 40 HOH HOH . J 6 HOH A 63 663 5 HOH HOH . J 6 HOH A 64 664 62 HOH HOH . J 6 HOH A 65 665 19 HOH HOH . J 6 HOH A 66 666 71 HOH HOH . J 6 HOH A 67 667 55 HOH HOH . J 6 HOH A 68 668 117 HOH HOH . J 6 HOH A 69 669 51 HOH HOH . J 6 HOH A 70 670 1 HOH HOH . J 6 HOH A 71 671 56 HOH HOH . J 6 HOH A 72 672 98 HOH HOH . J 6 HOH A 73 673 96 HOH HOH . J 6 HOH A 74 674 106 HOH HOH . J 6 HOH A 75 675 99 HOH HOH . J 6 HOH A 76 676 42 HOH HOH . J 6 HOH A 77 677 49 HOH HOH . J 6 HOH A 78 678 36 HOH HOH . J 6 HOH A 79 679 111 HOH HOH . J 6 HOH A 80 680 46 HOH HOH . J 6 HOH A 81 681 10 HOH HOH . J 6 HOH A 82 682 73 HOH HOH . J 6 HOH A 83 683 47 HOH HOH . J 6 HOH A 84 684 118 HOH HOH . J 6 HOH A 85 685 69 HOH HOH . J 6 HOH A 86 686 84 HOH HOH . J 6 HOH A 87 687 65 HOH HOH . J 6 HOH A 88 688 119 HOH HOH . J 6 HOH A 89 689 32 HOH HOH . J 6 HOH A 90 690 61 HOH HOH . J 6 HOH A 91 691 60 HOH HOH . J 6 HOH A 92 692 21 HOH HOH . J 6 HOH A 93 693 45 HOH HOH . J 6 HOH A 94 694 77 HOH HOH . J 6 HOH A 95 695 23 HOH HOH . J 6 HOH A 96 696 89 HOH HOH . J 6 HOH A 97 697 113 HOH HOH . J 6 HOH A 98 698 110 HOH HOH . J 6 HOH A 99 699 88 HOH HOH . J 6 HOH A 100 700 82 HOH HOH . J 6 HOH A 101 701 124 HOH HOH . J 6 HOH A 102 702 72 HOH HOH . J 6 HOH A 103 703 123 HOH HOH . J 6 HOH A 104 704 83 HOH HOH . J 6 HOH A 105 705 86 HOH HOH . J 6 HOH A 106 706 104 HOH HOH . J 6 HOH A 107 707 102 HOH HOH . J 6 HOH A 108 708 114 HOH HOH . J 6 HOH A 109 709 125 HOH HOH . J 6 HOH A 110 710 112 HOH HOH . K 6 HOH B 1 101 126 HOH HOH . K 6 HOH B 2 102 33 HOH HOH . K 6 HOH B 3 103 35 HOH HOH . K 6 HOH B 4 104 31 HOH HOH . K 6 HOH B 5 105 7 HOH HOH . K 6 HOH B 6 106 54 HOH HOH . K 6 HOH B 7 107 27 HOH HOH . K 6 HOH B 8 108 74 HOH HOH . K 6 HOH B 9 109 50 HOH HOH . K 6 HOH B 10 110 63 HOH HOH . K 6 HOH B 11 111 127 HOH HOH . K 6 HOH B 12 112 75 HOH HOH . K 6 HOH B 13 113 108 HOH HOH . K 6 HOH B 14 114 95 HOH HOH . K 6 HOH B 15 115 85 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 . . . C 3 -13.47 54.318 9.798 1 29.86 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . C 3 -13.736 54.086 8.425 1 30.58 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . C 3 -14.914 54.455 7.906 1 29.88 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . C 3 -15.85 55.053 8.667 1 31.91 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . C 3 -15.628 55.285 10.029 1 30.47 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . C 3 -14.401 54.912 10.573 1 30.81 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . C 3 -12.857 53.554 7.7 1 31.18 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . C 3 -16.93 55.394 8.152 1 30.39 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . C 3 -12.169 53.905 10.345 1 28.9 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . C 3 -11.259 55.085 10.693 1 27.54 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . C 3 -10.41 55.485 9.615 1 25.42 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . C 3 -10.445 54.538 11.844 1 27.49 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . C 3 -11.371 53.535 12.528 1 28.16 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . C 3 -12.359 53.194 11.571 1 28.61 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . C 3 -9.307 53.814 11.36 1 26.73 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . C 3 -12.062 54.091 13.769 1 27.67 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . C 3 -12.544 55.4 13.431 1 27.31 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . C 3 -13.276 56.345 14.513 1 25.27 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . C 3 -13.527 57.69 13.887 1 25.86 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . C 3 -14.494 55.58 15.022 1 25.62 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . C 3 -12.235 56.473 15.725 1 21.76 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . C 3 -10.711 56.965 15.757 1 23.02 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . C 3 -10.539 57.85 14.533 1 23.54 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . C 3 -10.635 57.705 17.075 1 23.45 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . C 3 -9.896 55.695 15.789 1 24.83 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #