data_6CDZ # _model_server_result.job_id OzFZeOfjyekBTNu27dv0Xw _model_server_result.datetime_utc '2024-11-23 19:20:41' _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 6cdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":702}' # _entry.id 6CDZ # _exptl.entry_id 6CDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 103.5 _cell.angle_gamma 90 _cell.entry_id 6CDZ _cell.length_a 67.658 _cell.length_b 80.451 _cell.length_c 94.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 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 covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 476 n n N1 C6 UMP sing 477 n n N1 C1' UMP sing 478 n n C2 N3 UMP sing 479 n n C2 O2 UMP doub 480 n n N3 C4 UMP sing 481 n n N3 HN3 UMP sing 482 n n C4 C5 UMP sing 483 n n C4 O4 UMP doub 484 n n C5 C6 UMP doub 485 n n C5 H5 UMP sing 486 n n C6 H6 UMP sing 487 n n C1' C2' UMP sing 488 n n C1' O4' UMP sing 489 n n C1' H1' UMP sing 490 n n C2' C3' UMP sing 491 n n C2' H2' UMP sing 492 n n C2' "H2''" UMP sing 493 n n C3' C4' UMP sing 494 n n C3' O3' UMP sing 495 n n C3' H3' UMP sing 496 n n C4' O4' UMP sing 497 n n C4' C5' UMP sing 498 n n C4' H4' UMP sing 499 n n O3' HO3' UMP sing 500 n n C5' O5' UMP sing 501 n n C5' H5' UMP sing 502 n n C5' "H5''" UMP sing 503 n n O5' P UMP sing 504 n n P OP1 UMP doub 505 n n P OP2 UMP sing 506 n n P OP3 UMP sing 507 n n OP2 HOP2 UMP sing 508 n n OP3 HOP3 UMP sing 509 n n # _atom_sites.entry_id 6CDZ _atom_sites.fract_transf_matrix[1][1] 0.01478 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003548 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01243 _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] 0.010931 _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 2 CB3 A 1 701 701 CB3 CB3 . D 3 UMP A 1 702 703 UMP UMP . E 2 CB3 B 1 301 702 CB3 CB3 . F 4 UMC B 1 302 704 UMC UMC . G 5 HOH A 1 801 27 HOH HOH . G 5 HOH A 2 802 118 HOH HOH . G 5 HOH A 3 803 61 HOH HOH . G 5 HOH A 4 804 98 HOH HOH . G 5 HOH A 5 805 122 HOH HOH . G 5 HOH A 6 806 67 HOH HOH . G 5 HOH A 7 807 9 HOH HOH . G 5 HOH A 8 808 54 HOH HOH . G 5 HOH A 9 809 1 HOH HOH . G 5 HOH A 10 810 109 HOH HOH . G 5 HOH A 11 811 32 HOH HOH . G 5 HOH A 12 812 34 HOH HOH . G 5 HOH A 13 813 26 HOH HOH . G 5 HOH A 14 814 13 HOH HOH . G 5 HOH A 15 815 5 HOH HOH . G 5 HOH A 16 816 56 HOH HOH . G 5 HOH A 17 817 65 HOH HOH . G 5 HOH A 18 818 152 HOH HOH . G 5 HOH A 19 819 60 HOH HOH . G 5 HOH A 20 820 53 HOH HOH . G 5 HOH A 21 821 161 HOH HOH . G 5 HOH A 22 822 165 HOH HOH . G 5 HOH A 23 823 11 HOH HOH . G 5 HOH A 24 824 23 HOH HOH . G 5 HOH A 25 825 78 HOH HOH . G 5 HOH A 26 826 16 HOH HOH . G 5 HOH A 27 827 157 HOH HOH . G 5 HOH A 28 828 162 HOH HOH . G 5 HOH A 29 829 138 HOH HOH . G 5 HOH A 30 830 89 HOH HOH . G 5 HOH A 31 831 92 HOH HOH . G 5 HOH A 32 832 21 HOH HOH . G 5 HOH A 33 833 31 HOH HOH . G 5 HOH A 34 834 42 HOH HOH . G 5 HOH A 35 835 63 HOH HOH . G 5 HOH A 36 836 15 HOH HOH . G 5 HOH A 37 837 77 HOH HOH . G 5 HOH A 38 838 4 HOH HOH . G 5 HOH A 39 839 124 HOH HOH . G 5 HOH A 40 840 90 HOH HOH . G 5 HOH A 41 841 46 HOH HOH . G 5 HOH A 42 842 108 HOH HOH . G 5 HOH A 43 843 28 HOH HOH . G 5 HOH A 44 844 69 HOH HOH . G 5 HOH A 45 845 166 HOH HOH . G 5 HOH A 46 846 70 HOH HOH . G 5 HOH A 47 847 75 HOH HOH . G 5 HOH A 48 848 86 HOH HOH . G 5 HOH A 49 849 12 HOH HOH . G 5 HOH A 50 850 128 HOH HOH . G 5 HOH A 51 851 19 HOH HOH . G 5 HOH A 52 852 3 HOH HOH . G 5 HOH A 53 853 119 HOH HOH . G 5 HOH A 54 854 139 HOH HOH . G 5 HOH A 55 855 37 HOH HOH . G 5 HOH A 56 856 68 HOH HOH . G 5 HOH A 57 857 130 HOH HOH . G 5 HOH A 58 858 48 HOH HOH . G 5 HOH A 59 859 58 HOH HOH . G 5 HOH A 60 860 147 HOH HOH . G 5 HOH A 61 861 49 HOH HOH . G 5 HOH A 62 862 163 HOH HOH . G 5 HOH A 63 863 47 HOH HOH . G 5 HOH A 64 864 8 HOH HOH . G 5 HOH A 65 865 20 HOH HOH . G 5 HOH A 66 866 112 HOH HOH . G 5 HOH A 67 867 59 HOH HOH . G 5 HOH A 68 868 135 HOH HOH . G 5 HOH A 69 869 137 HOH HOH . G 5 HOH A 70 870 66 HOH HOH . G 5 HOH A 71 871 125 HOH HOH . G 5 HOH A 72 872 38 HOH HOH . G 5 HOH A 73 873 111 HOH HOH . G 5 HOH A 74 874 156 HOH HOH . G 5 HOH A 75 875 116 HOH HOH . G 5 HOH A 76 876 133 HOH HOH . G 5 HOH A 77 877 84 HOH HOH . G 5 HOH A 78 878 64 HOH HOH . G 5 HOH A 79 879 144 HOH HOH . G 5 HOH A 80 880 91 HOH HOH . G 5 HOH A 81 881 97 HOH HOH . G 5 HOH A 82 882 41 HOH HOH . G 5 HOH A 83 883 94 HOH HOH . G 5 HOH A 84 884 146 HOH HOH . G 5 HOH A 85 885 115 HOH HOH . G 5 HOH A 86 886 95 HOH HOH . G 5 HOH A 87 887 110 HOH HOH . G 5 HOH A 88 888 151 HOH HOH . G 5 HOH A 89 889 149 HOH HOH . G 5 HOH A 90 890 141 HOH HOH . H 5 HOH B 1 401 160 HOH HOH . H 5 HOH B 2 402 154 HOH HOH . H 5 HOH B 3 403 72 HOH HOH . H 5 HOH B 4 404 35 HOH HOH . H 5 HOH B 5 405 164 HOH HOH . H 5 HOH B 6 406 52 HOH HOH . H 5 HOH B 7 407 131 HOH HOH . H 5 HOH B 8 408 57 HOH HOH . H 5 HOH B 9 409 55 HOH HOH . H 5 HOH B 10 410 18 HOH HOH . H 5 HOH B 11 411 74 HOH HOH . H 5 HOH B 12 412 167 HOH HOH . H 5 HOH B 13 413 40 HOH HOH . H 5 HOH B 14 414 83 HOH HOH . H 5 HOH B 15 415 105 HOH HOH . H 5 HOH B 16 416 96 HOH HOH . H 5 HOH B 17 417 2 HOH HOH . H 5 HOH B 18 418 6 HOH HOH . H 5 HOH B 19 419 140 HOH HOH . H 5 HOH B 20 420 117 HOH HOH . H 5 HOH B 21 421 159 HOH HOH . H 5 HOH B 22 422 62 HOH HOH . H 5 HOH B 23 423 80 HOH HOH . H 5 HOH B 24 424 148 HOH HOH . H 5 HOH B 25 425 158 HOH HOH . H 5 HOH B 26 426 85 HOH HOH . H 5 HOH B 27 427 25 HOH HOH . H 5 HOH B 28 428 22 HOH HOH . H 5 HOH B 29 429 106 HOH HOH . H 5 HOH B 30 430 10 HOH HOH . H 5 HOH B 31 431 44 HOH HOH . H 5 HOH B 32 432 82 HOH HOH . H 5 HOH B 33 433 79 HOH HOH . H 5 HOH B 34 434 145 HOH HOH . H 5 HOH B 35 435 30 HOH HOH . H 5 HOH B 36 436 33 HOH HOH . H 5 HOH B 37 437 14 HOH HOH . H 5 HOH B 38 438 99 HOH HOH . H 5 HOH B 39 439 81 HOH HOH . H 5 HOH B 40 440 143 HOH HOH . H 5 HOH B 41 441 39 HOH HOH . H 5 HOH B 42 442 45 HOH HOH . H 5 HOH B 43 443 29 HOH HOH . H 5 HOH B 44 444 155 HOH HOH . H 5 HOH B 45 445 129 HOH HOH . H 5 HOH B 46 446 17 HOH HOH . H 5 HOH B 47 447 36 HOH HOH . H 5 HOH B 48 448 7 HOH HOH . H 5 HOH B 49 449 121 HOH HOH . H 5 HOH B 50 450 51 HOH HOH . H 5 HOH B 51 451 127 HOH HOH . H 5 HOH B 52 452 43 HOH HOH . H 5 HOH B 53 453 71 HOH HOH . H 5 HOH B 54 454 113 HOH HOH . H 5 HOH B 55 455 87 HOH HOH . H 5 HOH B 56 456 50 HOH HOH . H 5 HOH B 57 457 120 HOH HOH . H 5 HOH B 58 458 107 HOH HOH . H 5 HOH B 59 459 102 HOH HOH . H 5 HOH B 60 460 93 HOH HOH . H 5 HOH B 61 461 142 HOH HOH . H 5 HOH B 62 462 88 HOH HOH . H 5 HOH B 63 463 103 HOH HOH . H 5 HOH B 64 464 24 HOH HOH . H 5 HOH B 65 465 114 HOH HOH . H 5 HOH B 66 466 104 HOH HOH . H 5 HOH B 67 467 136 HOH HOH . H 5 HOH B 68 468 132 HOH HOH . H 5 HOH B 69 469 126 HOH HOH . H 5 HOH B 70 470 150 HOH HOH . H 5 HOH B 71 471 153 HOH HOH . H 5 HOH B 72 472 123 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 UMP . . . D 3 1.67 6.298 33.801 1 32.49 ? N1 UMP 702 A 1 HETATM 2 C C2 UMP . . . D 3 2.542 5.402 34.384 1 31.19 ? C2 UMP 702 A 1 HETATM 3 N N3 UMP . . . D 3 2.45 4.054 34.094 1 31.27 ? N3 UMP 702 A 1 HETATM 4 C C4 UMP . . . D 3 1.482 3.601 33.22 1 30.63 ? C4 UMP 702 A 1 HETATM 5 C C5 UMP . . . D 3 0.604 4.506 32.636 1 31.5 ? C5 UMP 702 A 1 HETATM 6 C C6 UMP . . . D 3 0.708 5.86 32.936 1 32.76 ? C6 UMP 702 A 1 HETATM 7 O O2 UMP . . . D 3 3.402 5.809 35.166 1 28.93 ? O2 UMP 702 A 1 HETATM 8 O O4 UMP . . . D 3 1.398 2.402 32.959 1 28.49 ? O4 UMP 702 A 1 HETATM 9 C C1' UMP . . . D 3 1.781 7.732 34.131 1 32.96 ? C1' UMP 702 A 1 HETATM 10 C C2' UMP . . . D 3 3.03 8.355 33.524 1 31.23 ? C2' UMP 702 A 1 HETATM 11 C C3' UMP . . . D 3 2.57 9.762 33.194 1 32.5 ? C3' UMP 702 A 1 HETATM 12 C C4' UMP . . . D 3 1.066 9.651 33.009 1 35.38 ? C4' UMP 702 A 1 HETATM 13 O O3' UMP . . . D 3 2.881 10.644 34.249 1 32.31 ? O3' UMP 702 A 1 HETATM 14 O O4' UMP . . . D 3 0.663 8.45 33.64 1 35.49 ? O4' UMP 702 A 1 HETATM 15 C C5' UMP . . . D 3 0.689 9.625 31.533 1 31.23 ? C5' UMP 702 A 1 HETATM 16 O O5' UMP . . . D 3 0.995 10.874 30.954 1 32.58 ? O5' UMP 702 A 1 HETATM 17 P P UMP . . . D 3 1.682 10.955 29.499 1 33.34 ? P UMP 702 A 1 HETATM 18 O OP1 UMP . . . D 3 0.907 10.106 28.519 1 30.56 ? OP1 UMP 702 A 1 HETATM 19 O OP2 UMP . . . D 3 3.106 10.458 29.579 1 31.12 ? OP2 UMP 702 A 1 HETATM 20 O OP3 UMP . . . D 3 1.663 12.397 29.05 1 34.05 ? OP3 UMP 702 A 1 HETATM 21 H HN3 UMP . . . D 3 3.088 3.377 34.559 1 37.53 ? HN3 UMP 702 A 1 HETATM 22 H H5 UMP . . . D 3 -0.098 4.169 31.874 1 37.81 ? H5 UMP 702 A 1 HETATM 23 H H6 UMP . . . D 3 0.02 6.572 32.48 1 39.31 ? H6 UMP 702 A 1 HETATM 24 H H1' UMP . . . D 3 1.836 7.848 35.213 1 39.56 ? H1' UMP 702 A 1 HETATM 25 H H3' UMP . . . D 3 3.032 10.091 32.263 1 39 ? H3' UMP 702 A 1 HETATM 26 H H4' UMP . . . D 3 0.585 10.506 33.484 1 42.45 ? H4' UMP 702 A 1 HETATM 27 H HO3' UMP . . . D 3 2.052 10.996 34.636 1 38.78 ? HO3' UMP 702 A 1 HETATM 28 H H5' UMP . . . D 3 1.255 8.842 31.028 1 37.48 ? H5' UMP 702 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #