data_1YDZ # _model_server_result.job_id SoDDRHV1UBY41PlM4IbQQA _model_server_result.datetime_utc '2024-12-04 21:06:22' _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 1ydz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":150}' # _entry.id 1YDZ # _exptl.entry_id 1YDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 31.999 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'OXYGEN MOLECULE' _entity.pdbx_number_of_molecules 4 _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 1YDZ _cell.length_a 95.6 _cell.length_b 98.6 _cell.length_c 67.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N N ? 4 J N N ? 4 L 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 NE2 HIS 87 A HIS 87 1_555 E FE HEM . A HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 E FE HEM . A HEM 142 1_555 F O1 OXY . A OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? metalc ? metalc3 E FE HEM . A HEM 142 1_555 F O2 OXY . A OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc4 B NE2 HIS 92 B HIS 92 1_555 G FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc5 G FE HEM . B HEM 147 1_555 H O1 OXY . B OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.754 ? metalc ? metalc6 G FE HEM . B HEM 147 1_555 H O2 OXY . B OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc7 C NE2 HIS 87 C HIS 87 1_555 I FE HEM . C HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc8 I FE HEM . C HEM 142 1_555 J O1 OXY . C OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? metalc ? metalc9 I FE HEM . C HEM 142 1_555 J O2 OXY . C OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc10 D NE2 HIS 92 D HIS 92 1_555 K FE HEM . D HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc11 K FE HEM . D HEM 147 1_555 L O1 OXY . D OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? metalc ? metalc12 K FE HEM . D HEM 147 1_555 L O2 OXY . D OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? # _chem_comp.formula O2 _chem_comp.formula_weight 31.999 _chem_comp.id OXY _chem_comp.mon_nstd_flag . _chem_comp.name 'OXYGEN MOLECULE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _chem_comp_bond.atom_id_1 O1 _chem_comp_bond.atom_id_2 O2 _chem_comp_bond.comp_id OXY _chem_comp_bond.value_order doub _chem_comp_bond.pdbx_ordinal 298 _chem_comp_bond.pdbx_stereo_config n _chem_comp_bond.pdbx_aromatic_flag n # _atom_sites.entry_id 1YDZ _atom_sites.fract_transf_matrix[1][1] 0.01046 _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] 0.010142 _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] 0.014903 _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 E 3 HEM A 1 142 142 HEM HEM . F 4 OXY A 1 150 150 OXY O2 . G 3 HEM B 1 147 147 HEM HEM . H 4 OXY B 1 150 150 OXY O2 . I 3 HEM C 1 142 142 HEM HEM . J 4 OXY C 1 150 150 OXY O2 . K 3 HEM D 1 147 147 HEM HEM . L 4 OXY D 1 150 150 OXY O2 . M 5 HOH A 1 204 204 HOH HOH . M 5 HOH A 2 205 205 HOH HOH . M 5 HOH A 3 206 206 HOH HOH . M 5 HOH A 4 215 215 HOH HOH . M 5 HOH A 5 216 216 HOH HOH . M 5 HOH A 6 217 217 HOH HOH . M 5 HOH A 7 220 220 HOH HOH . M 5 HOH A 8 221 221 HOH HOH . M 5 HOH A 9 222 222 HOH HOH . M 5 HOH A 10 226 226 HOH HOH . M 5 HOH A 11 227 227 HOH HOH . M 5 HOH A 12 229 229 HOH HOH . M 5 HOH A 13 230 230 HOH HOH . M 5 HOH A 14 231 231 HOH HOH . M 5 HOH A 15 232 232 HOH HOH . M 5 HOH A 16 246 246 HOH HOH . M 5 HOH A 17 270 270 HOH HOH . M 5 HOH A 18 271 271 HOH HOH . M 5 HOH A 19 287 287 HOH HOH . M 5 HOH A 20 290 290 HOH HOH . M 5 HOH A 21 291 291 HOH HOH . M 5 HOH A 22 299 299 HOH HOH . M 5 HOH A 23 300 300 HOH HOH . M 5 HOH A 24 310 310 HOH HOH . M 5 HOH A 25 311 311 HOH HOH . M 5 HOH A 26 312 312 HOH HOH . M 5 HOH A 27 315 315 HOH HOH . M 5 HOH A 28 317 317 HOH HOH . M 5 HOH A 29 319 319 HOH HOH . M 5 HOH A 30 324 324 HOH HOH . M 5 HOH A 31 325 325 HOH HOH . M 5 HOH A 32 326 326 HOH HOH . M 5 HOH A 33 331 331 HOH HOH . M 5 HOH A 34 332 332 HOH HOH . M 5 HOH A 35 335 335 HOH HOH . M 5 HOH A 36 336 336 HOH HOH . M 5 HOH A 37 339 339 HOH HOH . M 5 HOH A 38 340 340 HOH HOH . M 5 HOH A 39 341 341 HOH HOH . M 5 HOH A 40 342 342 HOH HOH . M 5 HOH A 41 343 343 HOH HOH . M 5 HOH A 42 348 348 HOH HOH . M 5 HOH A 43 352 352 HOH HOH . M 5 HOH A 44 355 355 HOH HOH . M 5 HOH A 45 364 364 HOH HOH . M 5 HOH A 46 373 373 HOH HOH . M 5 HOH A 47 374 374 HOH HOH . M 5 HOH A 48 377 377 HOH HOH . M 5 HOH A 49 388 388 HOH HOH . M 5 HOH A 50 395 395 HOH HOH . M 5 HOH A 51 398 398 HOH HOH . M 5 HOH A 52 399 399 HOH HOH . M 5 HOH A 53 401 401 HOH HOH . M 5 HOH A 54 404 404 HOH HOH . M 5 HOH A 55 407 407 HOH HOH . M 5 HOH A 56 421 421 HOH HOH . M 5 HOH A 57 429 429 HOH HOH . M 5 HOH A 58 430 430 HOH HOH . M 5 HOH A 59 431 431 HOH HOH . N 5 HOH B 1 218 218 HOH HOH . N 5 HOH B 2 233 233 HOH HOH . N 5 HOH B 3 234 234 HOH HOH . N 5 HOH B 4 237 237 HOH HOH . N 5 HOH B 5 238 238 HOH HOH . N 5 HOH B 6 239 239 HOH HOH . N 5 HOH B 7 240 240 HOH HOH . N 5 HOH B 8 241 241 HOH HOH . N 5 HOH B 9 242 242 HOH HOH . N 5 HOH B 10 243 243 HOH HOH . N 5 HOH B 11 244 244 HOH HOH . N 5 HOH B 12 245 245 HOH HOH . N 5 HOH B 13 248 248 HOH HOH . N 5 HOH B 14 249 249 HOH HOH . N 5 HOH B 15 250 250 HOH HOH . N 5 HOH B 16 251 251 HOH HOH . N 5 HOH B 17 252 252 HOH HOH . N 5 HOH B 18 261 261 HOH HOH . N 5 HOH B 19 262 262 HOH HOH . N 5 HOH B 20 265 265 HOH HOH . N 5 HOH B 21 267 267 HOH HOH . N 5 HOH B 22 269 269 HOH HOH . N 5 HOH B 23 275 275 HOH HOH . N 5 HOH B 24 278 278 HOH HOH . N 5 HOH B 25 283 283 HOH HOH . N 5 HOH B 26 286 286 HOH HOH . N 5 HOH B 27 294 294 HOH HOH . N 5 HOH B 28 296 296 HOH HOH . N 5 HOH B 29 298 298 HOH HOH . N 5 HOH B 30 302 302 HOH HOH . N 5 HOH B 31 313 313 HOH HOH . N 5 HOH B 32 318 318 HOH HOH . N 5 HOH B 33 323 323 HOH HOH . N 5 HOH B 34 347 347 HOH HOH . N 5 HOH B 35 350 350 HOH HOH . N 5 HOH B 36 359 359 HOH HOH . N 5 HOH B 37 362 362 HOH HOH . N 5 HOH B 38 375 375 HOH HOH . N 5 HOH B 39 378 378 HOH HOH . N 5 HOH B 40 382 382 HOH HOH . N 5 HOH B 41 385 385 HOH HOH . N 5 HOH B 42 386 386 HOH HOH . N 5 HOH B 43 387 387 HOH HOH . N 5 HOH B 44 389 389 HOH HOH . N 5 HOH B 45 391 391 HOH HOH . N 5 HOH B 46 397 397 HOH HOH . N 5 HOH B 47 402 402 HOH HOH . N 5 HOH B 48 409 409 HOH HOH . N 5 HOH B 49 414 414 HOH HOH . N 5 HOH B 50 423 423 HOH HOH . N 5 HOH B 51 427 427 HOH HOH . O 5 HOH C 1 213 213 HOH HOH . O 5 HOH C 2 228 228 HOH HOH . O 5 HOH C 3 236 236 HOH HOH . O 5 HOH C 4 253 253 HOH HOH . O 5 HOH C 5 254 254 HOH HOH . O 5 HOH C 6 255 255 HOH HOH . O 5 HOH C 7 257 257 HOH HOH . O 5 HOH C 8 259 259 HOH HOH . O 5 HOH C 9 260 260 HOH HOH . O 5 HOH C 10 264 264 HOH HOH . O 5 HOH C 11 268 268 HOH HOH . O 5 HOH C 12 280 280 HOH HOH . O 5 HOH C 13 289 289 HOH HOH . O 5 HOH C 14 305 305 HOH HOH . O 5 HOH C 15 308 308 HOH HOH . O 5 HOH C 16 309 309 HOH HOH . O 5 HOH C 17 314 314 HOH HOH . O 5 HOH C 18 320 320 HOH HOH . O 5 HOH C 19 321 321 HOH HOH . O 5 HOH C 20 322 322 HOH HOH . O 5 HOH C 21 327 327 HOH HOH . O 5 HOH C 22 330 330 HOH HOH . O 5 HOH C 23 333 333 HOH HOH . O 5 HOH C 24 337 337 HOH HOH . O 5 HOH C 25 338 338 HOH HOH . O 5 HOH C 26 346 346 HOH HOH . O 5 HOH C 27 349 349 HOH HOH . O 5 HOH C 28 351 351 HOH HOH . O 5 HOH C 29 354 354 HOH HOH . O 5 HOH C 30 360 360 HOH HOH . O 5 HOH C 31 361 361 HOH HOH . O 5 HOH C 32 363 363 HOH HOH . O 5 HOH C 33 368 368 HOH HOH . O 5 HOH C 34 383 383 HOH HOH . O 5 HOH C 35 384 384 HOH HOH . O 5 HOH C 36 393 393 HOH HOH . O 5 HOH C 37 405 405 HOH HOH . O 5 HOH C 38 408 408 HOH HOH . O 5 HOH C 39 410 410 HOH HOH . O 5 HOH C 40 413 413 HOH HOH . O 5 HOH C 41 416 416 HOH HOH . O 5 HOH C 42 417 417 HOH HOH . O 5 HOH C 43 420 420 HOH HOH . O 5 HOH C 44 425 425 HOH HOH . O 5 HOH C 45 426 426 HOH HOH . O 5 HOH C 46 428 428 HOH HOH . O 5 HOH C 47 433 433 HOH HOH . O 5 HOH C 48 435 435 HOH HOH . P 5 HOH D 1 200 200 HOH HOH . P 5 HOH D 2 207 207 HOH HOH . P 5 HOH D 3 208 208 HOH HOH . P 5 HOH D 4 209 209 HOH HOH . P 5 HOH D 5 210 210 HOH HOH . P 5 HOH D 6 211 211 HOH HOH . P 5 HOH D 7 212 212 HOH HOH . P 5 HOH D 8 223 223 HOH HOH . P 5 HOH D 9 225 225 HOH HOH . P 5 HOH D 10 263 263 HOH HOH . P 5 HOH D 11 266 266 HOH HOH . P 5 HOH D 12 272 272 HOH HOH . P 5 HOH D 13 273 273 HOH HOH . P 5 HOH D 14 274 274 HOH HOH . P 5 HOH D 15 277 277 HOH HOH . P 5 HOH D 16 281 281 HOH HOH . P 5 HOH D 17 282 282 HOH HOH . P 5 HOH D 18 285 285 HOH HOH . P 5 HOH D 19 288 288 HOH HOH . P 5 HOH D 20 293 293 HOH HOH . P 5 HOH D 21 316 316 HOH HOH . P 5 HOH D 22 328 328 HOH HOH . P 5 HOH D 23 334 334 HOH HOH . P 5 HOH D 24 345 345 HOH HOH . P 5 HOH D 25 353 353 HOH HOH . P 5 HOH D 26 376 376 HOH HOH . P 5 HOH D 27 392 392 HOH HOH . P 5 HOH D 28 394 394 HOH HOH . P 5 HOH D 29 396 396 HOH HOH . P 5 HOH D 30 400 400 HOH HOH . P 5 HOH D 31 406 406 HOH HOH . P 5 HOH D 32 412 412 HOH HOH . P 5 HOH D 33 415 415 HOH HOH . P 5 HOH D 34 422 422 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 O1 OXY . . . F 4 9.551 42.164 -12.92 1 24.02 ? O1 OXY 150 A 1 HETATM 2 O O2 OXY . . . F 4 10.676 42.329 -13.137 1 24.47 ? O2 OXY 150 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 2 #