data_1F8Q # _model_server_result.job_id BGd2hOCDVxHBw_azgKuEtQ _model_server_result.datetime_utc '2024-11-13 18:42:46' _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 1f8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":367}' # _entry.id 1F8Q # _exptl.entry_id 1F8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 100.116 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PENTANEDIAL _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 120 _cell.entry_id 1F8Q _cell.length_a 131.51 _cell.length_b 131.51 _cell.length_c 39.81 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1F8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 XYS MAN C1 O1 . O2 HO2 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG B 301 NAG 2 n B NAG 2 B 2 NAG B 302 NAG 2 n B MAN 3 B 3 MAN B 303 MAN 2 n B XYS 4 B 4 XYS B 304 XYS # 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 ND2 ASN 227 A ASN 227 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale4 B O2 MAN . B MAN 3 1_555 B C1 XYS . B XYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? # _chem_comp.formula 'C5 H8 O2' _chem_comp.formula_weight 100.116 _chem_comp.id PTD _chem_comp.mon_nstd_flag . _chem_comp.name PENTANEDIAL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1F8Q _atom_sites.fract_transf_matrix[1][1] 0.007604 _atom_sites.fract_transf_matrix[1][2] 0.00439 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00878 _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] 0.025119 _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 3 PTD A 1 307 307 PTD PTD . D 3 PTD A 1 367 367 PTD PTD . E 3 PTD A 1 401 401 PTD PTD . F 4 CCN A 1 305 305 CCN CCN . G 4 CCN A 1 306 306 CCN CCN . H 5 HOH A 1 308 308 HOH HOH . H 5 HOH A 2 309 309 HOH HOH . H 5 HOH A 3 310 310 HOH HOH . H 5 HOH A 4 311 311 HOH HOH . H 5 HOH A 5 312 312 HOH HOH . H 5 HOH A 6 313 313 HOH HOH . H 5 HOH A 7 314 314 HOH HOH . H 5 HOH A 8 315 315 HOH HOH . H 5 HOH A 9 316 316 HOH HOH . H 5 HOH A 10 317 317 HOH HOH . H 5 HOH A 11 318 318 HOH HOH . H 5 HOH A 12 319 319 HOH HOH . H 5 HOH A 13 320 320 HOH HOH . H 5 HOH A 14 321 321 HOH HOH . H 5 HOH A 15 322 322 HOH HOH . H 5 HOH A 16 323 323 HOH HOH . H 5 HOH A 17 324 324 HOH HOH . H 5 HOH A 18 325 325 HOH HOH . H 5 HOH A 19 326 326 HOH HOH . H 5 HOH A 20 327 327 HOH HOH . H 5 HOH A 21 328 328 HOH HOH . H 5 HOH A 22 329 329 HOH HOH . H 5 HOH A 23 330 330 HOH HOH . H 5 HOH A 24 331 331 HOH HOH . H 5 HOH A 25 332 332 HOH HOH . H 5 HOH A 26 333 333 HOH HOH . H 5 HOH A 27 334 334 HOH HOH . H 5 HOH A 28 335 335 HOH HOH . H 5 HOH A 29 336 336 HOH HOH . H 5 HOH A 30 337 337 HOH HOH . H 5 HOH A 31 338 338 HOH HOH . H 5 HOH A 32 339 339 HOH HOH . H 5 HOH A 33 340 340 HOH HOH . H 5 HOH A 34 341 341 HOH HOH . H 5 HOH A 35 342 342 HOH HOH . H 5 HOH A 36 343 343 HOH HOH . H 5 HOH A 37 344 344 HOH HOH . H 5 HOH A 38 345 345 HOH HOH . H 5 HOH A 39 346 346 HOH HOH . H 5 HOH A 40 347 347 HOH HOH . H 5 HOH A 41 348 348 HOH HOH . H 5 HOH A 42 349 349 HOH HOH . H 5 HOH A 43 350 350 HOH HOH . H 5 HOH A 44 351 351 HOH HOH . H 5 HOH A 45 352 352 HOH HOH . H 5 HOH A 46 353 353 HOH HOH . H 5 HOH A 47 354 354 HOH HOH . H 5 HOH A 48 355 355 HOH HOH . H 5 HOH A 49 356 356 HOH HOH . H 5 HOH A 50 357 357 HOH HOH . H 5 HOH A 51 358 358 HOH HOH . H 5 HOH A 52 359 359 HOH HOH . H 5 HOH A 53 360 360 HOH HOH . H 5 HOH A 54 361 361 HOH HOH . H 5 HOH A 55 362 362 HOH HOH . H 5 HOH A 56 363 363 HOH HOH . H 5 HOH A 57 364 364 HOH HOH . H 5 HOH A 58 365 365 HOH HOH . H 5 HOH A 59 366 366 HOH HOH . H 5 HOH A 60 369 369 HOH HOH . H 5 HOH A 61 370 370 HOH HOH . H 5 HOH A 62 371 371 HOH HOH . H 5 HOH A 63 372 372 HOH HOH . H 5 HOH A 64 373 373 HOH HOH . H 5 HOH A 65 374 374 HOH HOH . H 5 HOH A 66 375 375 HOH HOH . H 5 HOH A 67 376 376 HOH HOH . H 5 HOH A 68 377 377 HOH HOH . H 5 HOH A 69 378 378 HOH HOH . H 5 HOH A 70 379 379 HOH HOH . H 5 HOH A 71 380 380 HOH HOH . H 5 HOH A 72 381 381 HOH HOH . H 5 HOH A 73 382 382 HOH HOH . H 5 HOH A 74 383 383 HOH HOH . H 5 HOH A 75 384 384 HOH HOH . H 5 HOH A 76 385 385 HOH HOH . H 5 HOH A 77 386 386 HOH HOH . H 5 HOH A 78 387 387 HOH HOH . H 5 HOH A 79 388 388 HOH HOH . H 5 HOH A 80 389 389 HOH HOH . H 5 HOH A 81 390 390 HOH HOH . H 5 HOH A 82 391 391 HOH HOH . H 5 HOH A 83 392 392 HOH HOH . H 5 HOH A 84 393 393 HOH HOH . H 5 HOH A 85 394 394 HOH HOH . H 5 HOH A 86 395 395 HOH HOH . H 5 HOH A 87 396 396 HOH HOH . H 5 HOH A 88 397 397 HOH HOH . H 5 HOH A 89 398 398 HOH HOH . H 5 HOH A 90 399 399 HOH HOH . H 5 HOH A 91 400 400 HOH HOH . H 5 HOH A 92 402 402 HOH HOH . H 5 HOH A 93 403 403 HOH HOH . H 5 HOH A 94 404 404 HOH HOH . H 5 HOH A 95 406 406 HOH HOH . H 5 HOH A 96 407 407 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 C C1 PTD . . . D 3 62.006 118.403 9.571 1 62.03 ? C1 PTD 367 A 1 HETATM 2 C C2 PTD . . . D 3 61.715 118.123 8.089 1 61.51 ? C2 PTD 367 A 1 HETATM 3 C C3 PTD . . . D 3 60.208 118.056 7.757 1 61.35 ? C3 PTD 367 A 1 HETATM 4 C C4 PTD . . . D 3 59.964 117.595 6.296 1 66.21 ? C4 PTD 367 A 1 HETATM 5 C C5 PTD . . . D 3 58.471 117.34 5.97 1 68.11 ? C5 PTD 367 A 1 HETATM 6 O O1 PTD . . . D 3 61.112 118.363 10.435 1 62.13 ? O1 PTD 367 A 1 HETATM 7 O O5 PTD . . . D 3 58.096 116.974 4.832 1 67.87 ? O5 PTD 367 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 7 #