data_8Y4W # _model_server_result.job_id fFMRoCrQN_c5mPFhiyBDRQ _model_server_result.datetime_utc '2025-03-22 22:42:02' _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 8y4w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":706}' # _entry.id 8Y4W # _exptl.entry_id 8Y4W _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 309.27 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-acetyl-beta-neuraminic acid' _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 90 _cell.entry_id 8Y4W _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y4W _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 ? _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 5 _struct_asym.id H _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 disulf ? disulf1 B SG CYS 22 B CYS 22 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 50 B CYS 50 1_555 B SG CYS 53 B CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A O SER 342 A SER 295 1_555 C NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc2 A O SER 345 A SER 298 1_555 C NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc3 A OE1 GLU 359 A GLU 312 1_555 E NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc4 A O THR 377 A THR 330 1_555 E NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.031 ? metalc ? metalc5 A O GLY 384 A GLY 337 1_555 C NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 A O VAL 387 A VAL 340 1_555 C NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc7 A O PRO 389 A PRO 342 1_555 C NA NA . A NA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc8 A O GLY 564 A GLY 517 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc9 A O MET 565 A MET 518 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.182 ? metalc ? metalc10 A O GLY 605 A GLY 558 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc11 A O THR 608 A THR 561 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc12 A OG1 THR 608 A THR 561 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc13 A O MET 611 A MET 564 1_555 D NA NA . A NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SLB _chem_comp.mon_nstd_flag . _chem_comp.name 'N-acetyl-beta-neuraminic acid' _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms 'N-acetylneuraminic acid;sialic acid;O-sialic acid;5-N-ACETYL-BETA-D-NEURAMINIC ACID;BETA-SIALIC ACID' # 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 C1 C2 SLB sing 417 n n C1 O1A SLB doub 418 n n C1 O1B SLB sing 419 n n C2 C3 SLB sing 420 n n C2 O2 SLB sing 421 n n C2 O6 SLB sing 422 n n C3 C4 SLB sing 423 n n C3 H32 SLB sing 424 n n C3 H31 SLB sing 425 n n C4 C5 SLB sing 426 n n C4 O4 SLB sing 427 n n C4 H4 SLB sing 428 n n C5 C6 SLB sing 429 n n C5 N5 SLB sing 430 n n C5 H5 SLB sing 431 n n C6 C7 SLB sing 432 n n C6 O6 SLB sing 433 n n C6 H6 SLB sing 434 n n C7 C8 SLB sing 435 n n C7 O7 SLB sing 436 n n C7 H7 SLB sing 437 n n C8 C9 SLB sing 438 n n C8 O8 SLB sing 439 n n C8 H8 SLB sing 440 n n C9 O9 SLB sing 441 n n C9 H92 SLB sing 442 n n C9 H91 SLB sing 443 n n C10 C11 SLB sing 444 n n C10 N5 SLB sing 445 n n C10 O10 SLB doub 446 n n C11 H111 SLB sing 447 n n C11 H113 SLB sing 448 n n C11 H112 SLB sing 449 n n N5 HN5 SLB sing 450 n n O1B HO1B SLB sing 451 n n O2 HO2 SLB sing 452 n n O4 HO4 SLB sing 453 n n O7 HO7 SLB sing 454 n n O8 HO8 SLB sing 455 n n O9 HO9 SLB sing 456 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version SLB DNeup5Acb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 SLB 'N-acetyl-b-D-neuraminic acid' 'COMMON NAME' GMML 1 SLB b-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 SLB Neu5Ac 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 8Y4W _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 C 3 NA A 1 701 1 NA NA . D 3 NA A 1 702 2 NA NA . E 3 NA A 1 703 3 NA NA . F 4 PTY A 1 704 1 PTY PTY . G 4 PTY A 1 705 2 PTY PTY . H 5 SLB A 1 706 1 SLB SLB . # 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 SLB . . . H 5 230.267 222.13 232.053 1 68.05 ? C1 SLB 706 A 1 HETATM 2 C C2 SLB . . . H 5 230.794 221.952 230.635 1 73.4 ? C2 SLB 706 A 1 HETATM 3 C C3 SLB . . . H 5 231.918 220.938 230.583 1 68.33 ? C3 SLB 706 A 1 HETATM 4 C C4 SLB . . . H 5 232.621 220.926 229.238 1 66.51 ? C4 SLB 706 A 1 HETATM 5 C C5 SLB . . . H 5 232.979 222.34 228.796 1 69.7 ? C5 SLB 706 A 1 HETATM 6 C C6 SLB . . . H 5 231.757 223.261 228.827 1 68.68 ? C6 SLB 706 A 1 HETATM 7 C C7 SLB . . . H 5 232.154 224.701 228.536 1 69.61 ? C7 SLB 706 A 1 HETATM 8 C C8 SLB . . . H 5 231.009 225.595 228.05 1 69.63 ? C8 SLB 706 A 1 HETATM 9 C C9 SLB . . . H 5 230.036 225.994 229.14 1 69.59 ? C9 SLB 706 A 1 HETATM 10 C C10 SLB . . . H 5 234.809 222.775 227.212 1 70.69 ? C10 SLB 706 A 1 HETATM 11 C C11 SLB . . . H 5 235.579 223.303 228.383 1 63.45 ? C11 SLB 706 A 1 HETATM 12 N N5 SLB . . . H 5 233.579 222.326 227.469 1 69.61 ? N5 SLB 706 A 1 HETATM 13 O O1A SLB . . . H 5 229.101 221.93 232.285 1 61.64 ? O1A SLB 706 A 1 HETATM 14 O O1B SLB . . . H 5 231.021 222.473 232.928 1 65.78 ? O1B SLB 706 A 1 HETATM 15 O O2 SLB . . . H 5 229.758 221.526 229.812 1 69.87 ? O2 SLB 706 A 1 HETATM 16 O O4 SLB . . . H 5 233.796 220.121 229.32 1 62.14 ? O4 SLB 706 A 1 HETATM 17 O O6 SLB . . . H 5 231.193 223.244 230.152 1 71.59 ? O6 SLB 706 A 1 HETATM 18 O O7 SLB . . . H 5 232.756 225.29 229.691 1 69.91 ? O7 SLB 706 A 1 HETATM 19 O O8 SLB . . . H 5 231.551 226.767 227.451 1 72.01 ? O8 SLB 706 A 1 HETATM 20 O O9 SLB . . . H 5 229.074 224.972 229.384 1 67.42 ? O9 SLB 706 A 1 HETATM 21 O O10 SLB . . . H 5 235.28 222.758 226.079 1 76.8 ? O10 SLB 706 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #