data_9GN4 # _model_server_result.job_id fBk_kvtEt1PUs6TUwMKedQ _model_server_result.datetime_utc '2024-12-26 17:07:53' _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 9gn4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 9GN4 # _exptl.entry_id 9GN4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _entity.pdbx_number_of_molecules 2 _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 9GN4 _cell.length_a 150.134 _cell.length_b 150.134 _cell.length_c 150.134 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GN4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id CTN _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTIDINE # 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 O5' C5' CTN sing 70 n n O5' H5' CTN sing 71 n n C5' C4' CTN sing 72 n n C5' "H5'1" CTN sing 73 n n C5' "H5'2" CTN sing 74 n n C4' O4' CTN sing 75 n n C4' C3' CTN sing 76 n n C4' H4' CTN sing 77 n n O4' C1' CTN sing 78 n n C1' N1 CTN sing 79 n n C1' C2' CTN sing 80 n n C1' H1' CTN sing 81 n n N1 C6 CTN sing 82 n y N1 C2 CTN sing 83 n y C6 C5 CTN doub 84 n y C6 H6 CTN sing 85 n n C5 C4 CTN sing 86 n y C5 H5 CTN sing 87 n n C4 N3 CTN doub 88 n y C4 N4 CTN sing 89 n n N3 C2 CTN sing 90 n y C2 O2 CTN doub 91 n n N4 HN41 CTN sing 92 n n N4 HN42 CTN sing 93 n n C2' O2' CTN sing 94 n n C2' C3' CTN sing 95 n n C2' H2' CTN sing 96 n n O2' H1 CTN sing 97 n n C3' O3' CTN sing 98 n n C3' H3' CTN sing 99 n n O3' H2 CTN sing 100 n n # _atom_sites.entry_id 9GN4 _atom_sites.fract_transf_matrix[1][1] 0.006661 _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] 0.006661 _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] 0.006661 _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 CTN A 1 201 201 CTN C . D 2 CTN B 1 201 201 CTN C . E 3 HOH A 1 301 88 HOH HOH . E 3 HOH A 2 302 139 HOH HOH . E 3 HOH A 3 303 167 HOH HOH . E 3 HOH A 4 304 144 HOH HOH . E 3 HOH A 5 305 55 HOH HOH . E 3 HOH A 6 306 114 HOH HOH . E 3 HOH A 7 307 6 HOH HOH . E 3 HOH A 8 308 44 HOH HOH . E 3 HOH A 9 309 127 HOH HOH . E 3 HOH A 10 310 120 HOH HOH . E 3 HOH A 11 311 136 HOH HOH . E 3 HOH A 12 312 111 HOH HOH . E 3 HOH A 13 313 118 HOH HOH . E 3 HOH A 14 314 39 HOH HOH . E 3 HOH A 15 315 19 HOH HOH . E 3 HOH A 16 316 13 HOH HOH . E 3 HOH A 17 317 12 HOH HOH . E 3 HOH A 18 318 24 HOH HOH . E 3 HOH A 19 319 14 HOH HOH . E 3 HOH A 20 320 3 HOH HOH . E 3 HOH A 21 321 132 HOH HOH . E 3 HOH A 22 322 145 HOH HOH . E 3 HOH A 23 323 52 HOH HOH . E 3 HOH A 24 324 113 HOH HOH . E 3 HOH A 25 325 140 HOH HOH . E 3 HOH A 26 326 28 HOH HOH . E 3 HOH A 27 327 123 HOH HOH . E 3 HOH A 28 328 43 HOH HOH . E 3 HOH A 29 329 115 HOH HOH . E 3 HOH A 30 330 171 HOH HOH . E 3 HOH A 31 331 170 HOH HOH . E 3 HOH A 32 332 153 HOH HOH . E 3 HOH A 33 333 130 HOH HOH . E 3 HOH A 34 334 106 HOH HOH . E 3 HOH A 35 335 11 HOH HOH . E 3 HOH A 36 336 21 HOH HOH . E 3 HOH A 37 337 154 HOH HOH . E 3 HOH A 38 338 109 HOH HOH . E 3 HOH A 39 339 63 HOH HOH . E 3 HOH A 40 340 117 HOH HOH . E 3 HOH A 41 341 110 HOH HOH . E 3 HOH A 42 342 108 HOH HOH . E 3 HOH A 43 343 80 HOH HOH . E 3 HOH A 44 344 124 HOH HOH . E 3 HOH A 45 345 17 HOH HOH . E 3 HOH A 46 346 32 HOH HOH . E 3 HOH A 47 347 160 HOH HOH . E 3 HOH A 48 348 173 HOH HOH . E 3 HOH A 49 349 51 HOH HOH . E 3 HOH A 50 350 133 HOH HOH . E 3 HOH A 51 351 5 HOH HOH . E 3 HOH A 52 352 131 HOH HOH . E 3 HOH A 53 353 18 HOH HOH . E 3 HOH A 54 354 148 HOH HOH . E 3 HOH A 55 355 112 HOH HOH . E 3 HOH A 56 356 34 HOH HOH . E 3 HOH A 57 357 168 HOH HOH . E 3 HOH A 58 358 119 HOH HOH . E 3 HOH A 59 359 135 HOH HOH . E 3 HOH A 60 360 116 HOH HOH . E 3 HOH A 61 361 128 HOH HOH . E 3 HOH A 62 363 164 HOH HOH . E 3 HOH A 63 364 121 HOH HOH . F 3 HOH B 1 301 146 HOH HOH . F 3 HOH B 2 302 125 HOH HOH . F 3 HOH B 3 303 126 HOH HOH . F 3 HOH B 4 304 143 HOH HOH . F 3 HOH B 5 305 161 HOH HOH . F 3 HOH B 6 306 151 HOH HOH . F 3 HOH B 7 307 101 HOH HOH . F 3 HOH B 8 308 165 HOH HOH . F 3 HOH B 9 309 66 HOH HOH . F 3 HOH B 10 310 53 HOH HOH . F 3 HOH B 11 311 30 HOH HOH . F 3 HOH B 12 312 105 HOH HOH . F 3 HOH B 13 313 134 HOH HOH . F 3 HOH B 14 314 158 HOH HOH . F 3 HOH B 15 315 33 HOH HOH . F 3 HOH B 16 316 107 HOH HOH . F 3 HOH B 17 317 152 HOH HOH . F 3 HOH B 18 318 20 HOH HOH . F 3 HOH B 19 319 137 HOH HOH . F 3 HOH B 20 320 31 HOH HOH . F 3 HOH B 21 321 82 HOH HOH . F 3 HOH B 22 322 159 HOH HOH . F 3 HOH B 23 323 2 HOH HOH . F 3 HOH B 24 324 157 HOH HOH . F 3 HOH B 25 325 104 HOH HOH . F 3 HOH B 26 326 155 HOH HOH . F 3 HOH B 27 327 4 HOH HOH . F 3 HOH B 28 328 102 HOH HOH . F 3 HOH B 29 329 156 HOH HOH . F 3 HOH B 30 330 172 HOH HOH . F 3 HOH B 31 331 36 HOH HOH . F 3 HOH B 32 332 10 HOH HOH . F 3 HOH B 33 333 8 HOH HOH . F 3 HOH B 34 334 26 HOH HOH . F 3 HOH B 35 335 163 HOH HOH . F 3 HOH B 36 336 35 HOH HOH . F 3 HOH B 37 337 48 HOH HOH . F 3 HOH B 38 338 141 HOH HOH . F 3 HOH B 39 339 103 HOH HOH . F 3 HOH B 40 340 138 HOH HOH . F 3 HOH B 41 341 175 HOH HOH . F 3 HOH B 42 342 42 HOH HOH . F 3 HOH B 43 343 100 HOH HOH . F 3 HOH B 44 344 174 HOH HOH . F 3 HOH B 45 345 166 HOH HOH . F 3 HOH B 46 346 142 HOH HOH . F 3 HOH B 47 347 122 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 O O5' CTN . . . D 2 7.077 19.63 -12.818 1 62.53 ? O5' CTN 201 B 1 HETATM 2 C C5' CTN . . . D 2 6.345 18.551 -13.499 1 86.14 ? C5' CTN 201 B 1 HETATM 3 C C4' CTN . . . D 2 5.613 17.675 -12.498 1 91.66 ? C4' CTN 201 B 1 HETATM 4 O O4' CTN . . . D 2 4.963 18.513 -11.497 1 92.24 ? O4' CTN 201 B 1 HETATM 5 C C1' CTN . . . D 2 3.55 18.426 -11.557 1 100.44 ? C1' CTN 201 B 1 HETATM 6 N N1 CTN . . . D 2 2.982 19.756 -11.98 1 105.42 ? N1 CTN 201 B 1 HETATM 7 C C6 CTN . . . D 2 3.828 20.832 -12.126 1 103.89 ? C6 CTN 201 B 1 HETATM 8 C C5 CTN . . . D 2 3.376 22.048 -12.49 1 104.79 ? C5 CTN 201 B 1 HETATM 9 C C4 CTN . . . D 2 1.967 22.208 -12.689 1 86.03 ? C4 CTN 201 B 1 HETATM 10 N N3 CTN . . . D 2 1.127 21.184 -12.53 1 92.15 ? N3 CTN 201 B 1 HETATM 11 C C2 CTN . . . D 2 1.588 19.955 -12.169 1 97.52 ? C2 CTN 201 B 1 HETATM 12 O O2 CTN . . . D 2 0.782 19.015 -12.055 1 71.41 ? O2 CTN 201 B 1 HETATM 13 N N4 CTN . . . D 2 1.435 23.371 -13.035 1 73.64 ? N4 CTN 201 B 1 HETATM 14 C C2' CTN . . . D 2 3.196 17.221 -12.449 1 89.94 ? C2' CTN 201 B 1 HETATM 15 O O2' CTN . . . D 2 2.652 16.218 -11.619 1 78.57 ? O2' CTN 201 B 1 HETATM 16 C C3' CTN . . . D 2 4.522 16.754 -13.091 1 100.3 ? C3' CTN 201 B 1 HETATM 17 O O3' CTN . . . D 2 4.759 15.355 -12.893 1 65.95 ? O3' CTN 201 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #