data_4WTA # _model_server_result.job_id 5tSSbRNaYC5FhjO8honz7g _model_server_result.datetime_utc '2024-11-09 02:09:26' _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 4wta # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":605}' # _entry.id 4WTA # _exptl.entry_id 4WTA _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 90 _cell.angle_gamma 120 _cell.entry_id 4WTA _cell.length_a 140.62 _cell.length_b 140.62 _cell.length_c 91 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WTA _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,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 5 _struct_asym.id H _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 B O3' U 8 P U 6 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 J O HOH . P HOH 101 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc3 C OD1 ASP 222 A ASP 220 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 C OD2 ASP 222 A ASP 220 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 C O THR 223 A THR 221 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc6 C OE2 GLU 239 A GLU 237 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc7 C ND1 HIS 256 A HIS 254 1_555 F MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc8 C OD1 ASP 320 A ASP 318 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc9 C OD2 ASP 320 A ASP 318 1_555 E MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc10 C OD1 ASP 321 A ASP 319 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc11 D MN MN . A MN 601 1_555 H O1A UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc12 E MN MN . A MN 602 1_555 H O1B UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc13 E MN MN . A MN 602 1_555 H O1A UDP . A UDP 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc14 E MN MN . A MN 602 1_555 K O HOH . A HOH 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? hydrog WATSON-CRICK hydrog1 A N1 A 3 T A 3 1_555 B N3 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 A 3 T A 3 1_555 B O4 U 8 P U 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 A 4 T A 4 1_555 B N3 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N6 A 4 T A 4 1_555 B O4 U 7 P U 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 A 5 T A 5 1_555 B N3 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N6 A 5 T A 5 1_555 B O4 U 6 P U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 6 T U 6 1_555 B N1 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 6 T U 6 1_555 B N6 A 5 P A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 T U 7 1_555 B N1 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 T U 7 1_555 B N6 A 4 P A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 468 n n N1 C6 UDP sing 469 n n N1 C1' UDP sing 470 n n C2 N3 UDP sing 471 n n C2 O2 UDP doub 472 n n N3 C4 UDP sing 473 n n N3 HN3 UDP sing 474 n n C4 C5 UDP sing 475 n n C4 O4 UDP doub 476 n n C5 C6 UDP doub 477 n n C5 H5 UDP sing 478 n n C6 H6 UDP sing 479 n n C1' C2' UDP sing 480 n n C1' O4' UDP sing 481 n n C1' H1' UDP sing 482 n n C2' O2' UDP sing 483 n n C2' C3' UDP sing 484 n n C2' H2' UDP sing 485 n n O2' HO2' UDP sing 486 n n C3' C4' UDP sing 487 n n C3' O3' UDP sing 488 n n C3' H3' UDP sing 489 n n C4' O4' UDP sing 490 n n C4' C5' UDP sing 491 n n C4' H4' UDP sing 492 n n O3' HO3' UDP sing 493 n n C5' O5' UDP sing 494 n n C5' "H5'1" UDP sing 495 n n C5' "H5'2" UDP sing 496 n n O5' PA UDP sing 497 n n PA O1A UDP doub 498 n n PA O2A UDP sing 499 n n PA O3A UDP sing 500 n n O2A HOA2 UDP sing 501 n n O3A PB UDP sing 502 n n PB O1B UDP doub 503 n n PB O2B UDP sing 504 n n PB O3B UDP sing 505 n n O2B HOB2 UDP sing 506 n n O3B HOB3 UDP sing 507 n n # _atom_sites.entry_id 4WTA _atom_sites.fract_transf_matrix[1][1] 0.007111 _atom_sites.fract_transf_matrix[1][2] 0.004106 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008211 _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] 0.010989 _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 3 MN A 1 601 1 MN MN . E 3 MN A 1 602 2 MN MN . F 3 MN A 1 603 3 MN MN . G 4 CL A 1 604 1 CL CL . H 5 UDP A 1 605 1 UDP UDP . I 6 HOH T 1 101 29 HOH HOH . J 6 HOH P 1 101 5 HOH HOH . J 6 HOH P 2 102 55 HOH HOH . J 6 HOH P 3 103 66 HOH HOH . K 6 HOH A 1 701 32 HOH HOH . K 6 HOH A 2 702 11 HOH HOH . K 6 HOH A 3 703 56 HOH HOH . K 6 HOH A 4 704 10 HOH HOH . K 6 HOH A 5 705 17 HOH HOH . K 6 HOH A 6 706 15 HOH HOH . K 6 HOH A 7 707 16 HOH HOH . K 6 HOH A 8 708 3 HOH HOH . K 6 HOH A 9 709 13 HOH HOH . K 6 HOH A 10 710 43 HOH HOH . K 6 HOH A 11 711 61 HOH HOH . K 6 HOH A 12 712 12 HOH HOH . K 6 HOH A 13 713 1 HOH HOH . K 6 HOH A 14 714 2 HOH HOH . K 6 HOH A 15 715 4 HOH HOH . K 6 HOH A 16 716 6 HOH HOH . K 6 HOH A 17 717 7 HOH HOH . K 6 HOH A 18 718 8 HOH HOH . K 6 HOH A 19 719 9 HOH HOH . K 6 HOH A 20 720 14 HOH HOH . K 6 HOH A 21 721 18 HOH HOH . K 6 HOH A 22 722 19 HOH HOH . K 6 HOH A 23 723 20 HOH HOH . K 6 HOH A 24 724 21 HOH HOH . K 6 HOH A 25 725 22 HOH HOH . K 6 HOH A 26 726 23 HOH HOH . K 6 HOH A 27 727 24 HOH HOH . K 6 HOH A 28 728 25 HOH HOH . K 6 HOH A 29 729 26 HOH HOH . K 6 HOH A 30 730 27 HOH HOH . K 6 HOH A 31 731 28 HOH HOH . K 6 HOH A 32 732 30 HOH HOH . K 6 HOH A 33 733 31 HOH HOH . K 6 HOH A 34 734 33 HOH HOH . K 6 HOH A 35 735 34 HOH HOH . K 6 HOH A 36 736 35 HOH HOH . K 6 HOH A 37 737 36 HOH HOH . K 6 HOH A 38 738 37 HOH HOH . K 6 HOH A 39 739 38 HOH HOH . K 6 HOH A 40 740 39 HOH HOH . K 6 HOH A 41 741 40 HOH HOH . K 6 HOH A 42 742 41 HOH HOH . K 6 HOH A 43 743 42 HOH HOH . K 6 HOH A 44 744 44 HOH HOH . K 6 HOH A 45 745 45 HOH HOH . K 6 HOH A 46 746 46 HOH HOH . K 6 HOH A 47 747 47 HOH HOH . K 6 HOH A 48 748 48 HOH HOH . K 6 HOH A 49 749 49 HOH HOH . K 6 HOH A 50 750 50 HOH HOH . K 6 HOH A 51 751 51 HOH HOH . K 6 HOH A 52 752 52 HOH HOH . K 6 HOH A 53 753 53 HOH HOH . K 6 HOH A 54 754 54 HOH HOH . K 6 HOH A 55 755 57 HOH HOH . K 6 HOH A 56 756 58 HOH HOH . K 6 HOH A 57 757 59 HOH HOH . K 6 HOH A 58 758 60 HOH HOH . K 6 HOH A 59 759 62 HOH HOH . K 6 HOH A 60 760 63 HOH HOH . K 6 HOH A 61 761 64 HOH HOH . K 6 HOH A 62 762 65 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 . . . H 5 40.002 -46.115 7.263 1 47.57 ? N1 UDP 605 A 1 HETATM 2 C C2 UDP . . . H 5 39.173 -46.039 8.417 1 51.69 ? C2 UDP 605 A 1 HETATM 3 N N3 UDP . . . H 5 39.629 -45.544 9.564 1 54.88 ? N3 UDP 605 A 1 HETATM 4 C C4 UDP . . . H 5 40.888 -45.085 9.648 1 55.13 ? C4 UDP 605 A 1 HETATM 5 C C5 UDP . . . H 5 41.738 -45.129 8.527 1 52.66 ? C5 UDP 605 A 1 HETATM 6 C C6 UDP . . . H 5 41.259 -45.645 7.318 1 49.39 ? C6 UDP 605 A 1 HETATM 7 O O2 UDP . . . H 5 38 -46.445 8.405 1 52.1 ? O2 UDP 605 A 1 HETATM 8 O O4 UDP . . . H 5 41.272 -44.619 10.749 1 52.03 ? O4 UDP 605 A 1 HETATM 9 C C1' UDP . . . H 5 39.431 -46.636 6.029 1 44.37 ? C1' UDP 605 A 1 HETATM 10 C C2' UDP . . . H 5 38.806 -45.435 5.333 1 45.63 ? C2' UDP 605 A 1 HETATM 11 O O2' UDP . . . H 5 37.553 -45.77 4.706 1 47.33 ? O2' UDP 605 A 1 HETATM 12 C C3' UDP . . . H 5 39.863 -45.041 4.334 1 44.63 ? C3' UDP 605 A 1 HETATM 13 C C4' UDP . . . H 5 40.418 -46.387 3.928 1 45.13 ? C4' UDP 605 A 1 HETATM 14 O O4' UDP . . . H 5 40.4 -47.151 5.14 1 43.98 ? O4' UDP 605 A 1 HETATM 15 O O3' UDP . . . H 5 39.326 -44.289 3.247 1 47.14 ? O3' UDP 605 A 1 HETATM 16 C C5' UDP . . . H 5 41.812 -46.341 3.293 1 46.52 ? C5' UDP 605 A 1 HETATM 17 O O5' UDP . . . H 5 42.773 -45.795 4.216 1 48.72 ? O5' UDP 605 A 1 HETATM 18 P PA UDP . . . H 5 43.992 -44.854 3.765 1 43.72 ? PA UDP 605 A 1 HETATM 19 O O1A UDP . . . H 5 44.435 -45.269 2.38 1 45.24 ? O1A UDP 605 A 1 HETATM 20 O O2A UDP . . . H 5 44.941 -45.019 4.903 1 47.87 ? O2A UDP 605 A 1 HETATM 21 O O3A UDP . . . H 5 43.319 -43.382 3.749 1 40.22 ? O3A UDP 605 A 1 HETATM 22 P PB UDP . . . H 5 42.473 -42.756 2.49 1 43.84 ? PB UDP 605 A 1 HETATM 23 O O1B UDP . . . H 5 42.651 -43.71 1.325 1 32.28 ? O1B UDP 605 A 1 HETATM 24 O O2B UDP . . . H 5 43.001 -41.316 2.394 1 40 ? O2B UDP 605 A 1 HETATM 25 O O3B UDP . . . H 5 41.016 -42.658 2.911 1 42.14 ? O3B UDP 605 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #