data_1YI4 # _model_server_result.job_id aGQirA_vHdeWgKRq0Y64PA _model_server_result.datetime_utc '2024-11-27 04:36:38' _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 1yi4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":306}' # _entry.id 1YI4 # _exptl.entry_id 1YI4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _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 1YI4 _cell.length_a 98.269 _cell.length_b 98.269 _cell.length_c 80.386 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YI4 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 ASN 128 A ASN 160 1_555 A N CME 129 A CME 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C CME 129 A CME 161 1_555 A N GLY 130 A GLY 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C SER 228 A SER 260 1_555 A N SEP 229 A SEP 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 229 A SEP 261 1_555 A N GLU 230 A GLU 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 1YI4 _atom_sites.fract_transf_matrix[1][1] 0.010176 _atom_sites.fract_transf_matrix[1][2] 0.005875 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01175 _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] 0.01244 _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 B 2 ADN A 1 306 201 ADN ADN . C 3 HOH A 1 307 1 HOH HOH . C 3 HOH A 2 308 2 HOH HOH . C 3 HOH A 3 309 3 HOH HOH . C 3 HOH A 4 310 4 HOH HOH . C 3 HOH A 5 311 5 HOH HOH . C 3 HOH A 6 312 6 HOH HOH . C 3 HOH A 7 313 7 HOH HOH . C 3 HOH A 8 314 8 HOH HOH . C 3 HOH A 9 315 9 HOH HOH . C 3 HOH A 10 316 10 HOH HOH . C 3 HOH A 11 317 11 HOH HOH . C 3 HOH A 12 318 12 HOH HOH . C 3 HOH A 13 319 13 HOH HOH . C 3 HOH A 14 320 14 HOH HOH . C 3 HOH A 15 321 15 HOH HOH . C 3 HOH A 16 322 16 HOH HOH . C 3 HOH A 17 323 17 HOH HOH . C 3 HOH A 18 324 18 HOH HOH . C 3 HOH A 19 325 19 HOH HOH . C 3 HOH A 20 326 20 HOH HOH . C 3 HOH A 21 327 21 HOH HOH . C 3 HOH A 22 328 22 HOH HOH . C 3 HOH A 23 329 23 HOH HOH . C 3 HOH A 24 330 24 HOH HOH . C 3 HOH A 25 331 25 HOH HOH . C 3 HOH A 26 332 26 HOH HOH . C 3 HOH A 27 333 27 HOH HOH . C 3 HOH A 28 334 28 HOH HOH . C 3 HOH A 29 335 29 HOH HOH . C 3 HOH A 30 336 30 HOH HOH . C 3 HOH A 31 337 31 HOH HOH . C 3 HOH A 32 338 32 HOH HOH . C 3 HOH A 33 339 33 HOH HOH . C 3 HOH A 34 340 34 HOH HOH . C 3 HOH A 35 341 35 HOH HOH . C 3 HOH A 36 342 36 HOH HOH . C 3 HOH A 37 343 37 HOH HOH . C 3 HOH A 38 344 38 HOH HOH . C 3 HOH A 39 345 39 HOH HOH . C 3 HOH A 40 346 40 HOH HOH . C 3 HOH A 41 347 41 HOH HOH . C 3 HOH A 42 348 42 HOH HOH . C 3 HOH A 43 349 43 HOH HOH . C 3 HOH A 44 350 44 HOH HOH . C 3 HOH A 45 351 45 HOH HOH . C 3 HOH A 46 352 46 HOH HOH . C 3 HOH A 47 353 48 HOH HOH . C 3 HOH A 48 354 49 HOH HOH . C 3 HOH A 49 355 50 HOH HOH . C 3 HOH A 50 356 51 HOH HOH . C 3 HOH A 51 357 52 HOH HOH . C 3 HOH A 52 358 53 HOH HOH . C 3 HOH A 53 359 54 HOH HOH . C 3 HOH A 54 360 55 HOH HOH . C 3 HOH A 55 361 56 HOH HOH . C 3 HOH A 56 362 57 HOH HOH . C 3 HOH A 57 363 58 HOH HOH . C 3 HOH A 58 364 59 HOH HOH . C 3 HOH A 59 365 60 HOH HOH . C 3 HOH A 60 366 61 HOH HOH . C 3 HOH A 61 367 62 HOH HOH . C 3 HOH A 62 368 63 HOH HOH . C 3 HOH A 63 369 64 HOH HOH . C 3 HOH A 64 370 65 HOH HOH . C 3 HOH A 65 371 66 HOH HOH . C 3 HOH A 66 372 67 HOH HOH . C 3 HOH A 67 373 68 HOH HOH . C 3 HOH A 68 374 69 HOH HOH . C 3 HOH A 69 375 70 HOH HOH . C 3 HOH A 70 376 71 HOH HOH . C 3 HOH A 71 377 72 HOH HOH . C 3 HOH A 72 378 73 HOH HOH . C 3 HOH A 73 379 74 HOH HOH . C 3 HOH A 74 380 75 HOH HOH . C 3 HOH A 75 381 76 HOH HOH . C 3 HOH A 76 382 77 HOH HOH . C 3 HOH A 77 383 78 HOH HOH . C 3 HOH A 78 384 79 HOH HOH . C 3 HOH A 79 385 80 HOH HOH . C 3 HOH A 80 386 81 HOH HOH . C 3 HOH A 81 387 82 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' ADN . . . B 2 -16.339 36.219 -4.866 1 90.35 ? O5' ADN 306 A 1 HETATM 2 C C5' ADN . . . B 2 -17.619 35.66 -4.722 1 89.13 ? C5' ADN 306 A 1 HETATM 3 C C4' ADN . . . B 2 -18.711 36.734 -4.721 1 88.6 ? C4' ADN 306 A 1 HETATM 4 O O4' ADN . . . B 2 -19.703 36.424 -3.759 1 87.71 ? O4' ADN 306 A 1 HETATM 5 C C3' ADN . . . B 2 -18.223 38.128 -4.344 1 88.61 ? C3' ADN 306 A 1 HETATM 6 O O3' ADN . . . B 2 -17.746 38.829 -5.506 1 90.22 ? O3' ADN 306 A 1 HETATM 7 C C2' ADN . . . B 2 -19.483 38.766 -3.796 1 88.11 ? C2' ADN 306 A 1 HETATM 8 O O2' ADN . . . B 2 -20.235 39.239 -4.88 1 87.98 ? O2' ADN 306 A 1 HETATM 9 C C1' ADN . . . B 2 -20.212 37.595 -3.129 1 86.86 ? C1' ADN 306 A 1 HETATM 10 N N9 ADN . . . B 2 -19.913 37.547 -1.682 1 84.51 ? N9 ADN 306 A 1 HETATM 11 C C8 ADN . . . B 2 -19.064 36.756 -0.99 1 83.35 ? C8 ADN 306 A 1 HETATM 12 N N7 ADN . . . B 2 -19.039 37.003 0.337 1 82.69 ? N7 ADN 306 A 1 HETATM 13 C C5 ADN . . . B 2 -19.949 38.036 0.52 1 82.59 ? C5 ADN 306 A 1 HETATM 14 C C6 ADN . . . B 2 -20.401 38.741 1.595 1 81.98 ? C6 ADN 306 A 1 HETATM 15 N N6 ADN . . . B 2 -19.937 38.487 2.83 1 82.45 ? N6 ADN 306 A 1 HETATM 16 N N1 ADN . . . B 2 -21.32 39.711 1.479 1 81.6 ? N1 ADN 306 A 1 HETATM 17 C C2 ADN . . . B 2 -21.794 39.981 0.251 1 82.32 ? C2 ADN 306 A 1 HETATM 18 N N3 ADN . . . B 2 -21.418 39.353 -0.867 1 82.43 ? N3 ADN 306 A 1 HETATM 19 C C4 ADN . . . B 2 -20.494 38.379 -0.732 1 83.57 ? C4 ADN 306 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #