data_8TZ5 # _model_server_result.job_id Addu2vUAO3t3uHiJVxQdhw _model_server_result.datetime_utc '2024-10-25 20:28:39' _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 8tz5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":801}' # _entry.id 8TZ5 # _exptl.entry_id 8TZ5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 259.216 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-hydroxycytidine _entity.pdbx_number_of_molecules 3 _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 8TZ5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TZ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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,J,K,L,M,N,O,P,Q,R,S,T,U _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 J N N ? 2 P N 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 O ASN 357 A ASN 342 1_555 E NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc2 A OD1 ASN 357 A ASN 342 1_555 E NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 A O ILE 360 A ILE 345 1_555 E NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc4 A OG1 THR 391 A THR 376 1_555 E NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc5 A O ILE 392 A ILE 377 1_555 E NA NA . A NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc6 B O ASN 357 B ASN 342 1_555 K NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc7 B OD1 ASN 357 B ASN 342 1_555 K NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc8 B O ILE 360 B ILE 345 1_555 K NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc9 B OG1 THR 391 B THR 376 1_555 K NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc10 B O ILE 392 B ILE 377 1_555 K NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.027 ? metalc ? metalc11 C O ASN 357 C ASN 342 1_555 Q NA NA . C NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc12 C OD1 ASN 357 C ASN 342 1_555 Q NA NA . C NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc13 C O ILE 360 C ILE 345 1_555 Q NA NA . C NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc14 C OG1 THR 391 C THR 376 1_555 Q NA NA . C NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc15 C O ILE 392 C ILE 377 1_555 Q NA NA . C NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.027 ? # _chem_comp.formula 'C9 H13 N3 O6' _chem_comp.formula_weight 259.216 _chem_comp.id U56 _chem_comp.mon_nstd_flag . _chem_comp.name N-hydroxycytidine _chem_comp.type non-polymer _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 O01 C02 U56 doub 489 n n N03 C02 U56 sing 490 n n N03 C04 U56 doub 491 n n C02 N09 U56 sing 492 n n N05 C04 U56 sing 493 n n N05 O06 U56 sing 494 n n O18 C17 U56 sing 495 n n C04 C07 U56 sing 496 n n N09 C10 U56 sing 497 n n N09 C08 U56 sing 498 n n C17 C10 U56 sing 499 n n C17 C15 U56 sing 500 n n C10 O11 U56 sing 501 n n C07 C08 U56 doub 502 n n O16 C15 U56 sing 503 n n C15 C12 U56 sing 504 n n O11 C12 U56 sing 505 n n C12 C13 U56 sing 506 n n C13 O14 U56 sing 507 n n C10 H101 U56 sing 508 n n C07 H071 U56 sing 509 n n C08 H081 U56 sing 510 n n C12 H121 U56 sing 511 n n C13 H131 U56 sing 512 n n C13 H132 U56 sing 513 n n C15 H151 U56 sing 514 n n C17 H171 U56 sing 515 n n N05 H051 U56 sing 516 n n O06 H061 U56 sing 517 n n O14 H141 U56 sing 518 n n O16 H161 U56 sing 519 n n O18 H181 U56 sing 520 n n # _atom_sites.entry_id 8TZ5 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 U56 A 1 801 701 U56 NHC . E 3 NA A 1 802 801 NA NA . F 4 LBN A 1 803 1001 LBN LBN . G 4 LBN A 1 804 1002 LBN LBN . H 4 LBN A 1 805 1003 LBN LBN . I 4 LBN A 1 806 1004 LBN LBN . J 2 U56 B 1 801 701 U56 NHC . K 3 NA B 1 802 801 NA NA . L 4 LBN B 1 803 1001 LBN LBN . M 4 LBN B 1 804 1002 LBN LBN . N 4 LBN B 1 805 1003 LBN LBN . O 4 LBN B 1 806 1004 LBN LBN . P 2 U56 C 1 801 701 U56 NHC . Q 3 NA C 1 802 801 NA NA . R 4 LBN C 1 803 1001 LBN LBN . S 4 LBN C 1 804 1002 LBN LBN . T 4 LBN C 1 805 1003 LBN LBN . U 4 LBN C 1 806 1004 LBN LBN . # 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 C C10 U56 . . . J 2 126.939 134.797 140.22 1 33.99 ? C10 U56 801 B 1 HETATM 2 C C02 U56 . . . J 2 127.877 133.15 138.538 1 29.64 ? C02 U56 801 B 1 HETATM 3 C C04 U56 . . . J 2 129.287 131.197 139.34 1 31.01 ? C04 U56 801 B 1 HETATM 4 C C07 U56 . . . J 2 129.118 131.665 140.738 1 31.38 ? C07 U56 801 B 1 HETATM 5 C C08 U56 . . . J 2 128.319 132.89 141.022 1 30.48 ? C08 U56 801 B 1 HETATM 6 C C12 U56 . . . J 2 125.929 135.497 142.093 1 30.86 ? C12 U56 801 B 1 HETATM 7 C C13 U56 . . . J 2 126.002 135.163 143.461 1 33.01 ? C13 U56 801 B 1 HETATM 8 C C15 U56 . . . J 2 124.917 134.541 141.378 1 30.22 ? C15 U56 801 B 1 HETATM 9 C C17 U56 . . . J 2 125.343 134.418 140.21 1 30.31 ? C17 U56 801 B 1 HETATM 10 N N03 U56 . . . J 2 128.672 131.933 138.252 1 28.44 ? N03 U56 801 B 1 HETATM 11 N N05 U56 . . . J 2 130.052 130.027 139.074 1 37.91 ? N05 U56 801 B 1 HETATM 12 N N09 U56 . . . J 2 127.707 133.622 139.937 1 28.68 ? N09 U56 801 B 1 HETATM 13 O O01 U56 . . . J 2 127.378 133.745 137.651 1 38.8 ? O01 U56 801 B 1 HETATM 14 O O06 U56 . . . J 2 130.636 129.334 140.134 1 34.84 ? O06 U56 801 B 1 HETATM 15 O O11 U56 . . . J 2 127.239 135.237 141.399 1 38.68 ? O11 U56 801 B 1 HETATM 16 O O14 U56 . . . J 2 126.51 133.869 143.571 1 27.26 ? O14 U56 801 B 1 HETATM 17 O O16 U56 . . . J 2 123.539 135.156 141.368 1 32.41 ? O16 U56 801 B 1 HETATM 18 O O18 U56 . . . J 2 124.615 135.34 139.307 1 30.66 ? O18 U56 801 B 1 HETATM 19 H H101 U56 . . . J 2 127.138 135.564 139.482 1 31.28 ? H101 U56 801 B 1 HETATM 20 H H071 U56 . . . J 2 129.574 131.122 141.547 1 30.33 ? H071 U56 801 B 1 HETATM 21 H H081 U56 . . . J 2 128.196 133.233 142.044 1 30.01 ? H081 U56 801 B 1 HETATM 22 H H121 U56 . . . J 2 125.636 136.521 141.962 1 30.35 ? H121 U56 801 B 1 HETATM 23 H H131 U56 . . . J 2 124.997 135.197 143.901 1 30.33 ? H131 U56 801 B 1 HETATM 24 H H132 U56 . . . J 2 126.651 135.857 143.977 1 30.73 ? H132 U56 801 B 1 HETATM 25 H H151 U56 . . . J 2 124.901 133.579 141.88 1 29.95 ? H151 U56 801 B 1 HETATM 26 H H171 U56 . . . J 2 125.212 133.388 139.879 1 30.24 ? H171 U56 801 B 1 HETATM 27 H H051 U56 . . . J 2 130.171 129.703 138.125 1 31.66 ? H051 U56 801 B 1 HETATM 28 H H061 U56 . . . J 2 130.837 128.448 139.872 1 30.98 ? H061 U56 801 B 1 HETATM 29 H H141 U56 . . . J 2 125.972 133.373 144.177 1 29.27 ? H141 U56 801 B 1 HETATM 30 H H161 U56 . . . J 2 122.995 134.71 141.994 1 28.98 ? H161 U56 801 B 1 HETATM 31 H H181 U56 . . . J 2 124.818 135.126 138.417 1 30.87 ? H181 U56 801 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #