data_4WRL # _model_server_result.job_id AAjMYrVZNVrnE7wVV4wH3w _model_server_result.datetime_utc '2025-07-04 21:48:49' _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 4wrl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":407}' # _entry.id 4WRL # _exptl.entry_id 4WRL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-acetyl-alpha-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 4WRL _cell.length_a 142.997 _cell.length_b 142.997 _cell.length_c 138.323 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WRL _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details software_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 _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 6 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . sing 3 ? 3 4 1 FUC NAG C1 O1 . O6 HO6 . sing 4 ? 4 2 1 GAL NAG C1 O1 . O4 HO4 . sing 5 ? 5 2 1 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 5 3 2 SIA GAL C2 O2 . O3 HO3 . 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 3 n E NAG 1 E 1 NAG A 401 NAG 3 n E GAL 2 E 2 GAL A 403 GAL 3 n E SIA 3 E 3 SIA A 404 SIA 3 n E FUC 4 E 4 FUC A 402 FUC 4 n F NAG 1 F 1 NAG A 405 NAG 4 n F GAL 2 F 2 GAL A 406 GAL 5 n G NAG 1 G 1 NAG A 409 NAG 5 n G GAL 2 G 2 GAL A 410 GAL 5 n G SIA 3 G 3 SIA A 411 SIA 3 n H NAG 1 H 1 NAG C 401 NAG 3 n H GAL 2 H 2 GAL C 403 GAL 3 n H SIA 3 H 3 SIA C 404 SIA 3 n H FUC 4 H 4 FUC C 402 FUC 5 n I NAG 1 I 1 NAG C 407 NAG 5 n I GAL 2 I 2 GAL C 408 GAL 5 n I SIA 3 I 3 SIA C 409 SIA # 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 A SG CYS 23 A CYS 42 1_555 A SG CYS 65 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 108 A CYS 127 1_555 A SG CYS 158 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 205 A CYS 224 1_555 A SG CYS 259 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 23 C CYS 42 1_555 B SG CYS 65 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 108 C CYS 127 1_555 B SG CYS 158 C CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 205 C CYS 224 1_555 B SG CYS 259 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 28 B CYS 7 1_555 C SG CYS 111 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 52 B CYS 31 1_555 D SG CYS 52 D CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 69 B CYS 48 1_555 C SG CYS 160 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 123 B CYS 102 1_555 C SG CYS 167 B CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 D SG CYS 28 D CYS 7 1_555 D SG CYS 111 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 D SG CYS 69 D CYS 48 1_555 D SG CYS 160 D CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 D SG CYS 123 D CYS 102 1_555 D SG CYS 167 D CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 26 A ASN 45 1_555 K C1 NAG . A NAG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 54 A ASN 73 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale3 A ND2 ASN 134 A ASN 153 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale4 A ND2 ASN 256 A ASN 275 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 B ND2 ASN 26 C ASN 45 1_555 M C1 NAG . C NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 B ND2 ASN 54 C ASN 73 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale7 B ND2 ASN 134 C ASN 153 1_555 L C1 NAG . C NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 256 C ASN 275 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 GAL . E GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale10 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale11 E O3 GAL . E GAL 2 1_555 E C2 SIA . E SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale14 G O3 GAL . G GAL 2 1_555 G C2 SIA . G SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale15 H O4 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale16 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 H O3 GAL . H GAL 2 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale18 I O4 NAG . I NAG 1 1_555 I C1 GAL . I GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale19 I O3 GAL . I GAL 2 1_555 I C2 SIA . I SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? # _chem_comp.formula 'C11 H19 N O9' _chem_comp.formula_weight 309.27 _chem_comp.id SIA _chem_comp.mon_nstd_flag . _chem_comp.name 'N-acetyl-alpha-neuraminic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 'N-acetylneuraminic acid;sialic acid;alpha-sialic acid;O-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 SIA sing 365 n n C1 O1A SIA doub 366 n n C1 O1B SIA sing 367 n n C2 C3 SIA sing 368 n n C2 O2 SIA sing 369 n n C2 O6 SIA sing 370 n n C3 C4 SIA sing 371 n n C3 H32 SIA sing 372 n n C3 H31 SIA sing 373 n n C4 C5 SIA sing 374 n n C4 O4 SIA sing 375 n n C4 H4 SIA sing 376 n n C5 C6 SIA sing 377 n n C5 N5 SIA sing 378 n n C5 H5 SIA sing 379 n n C6 C7 SIA sing 380 n n C6 O6 SIA sing 381 n n C6 H6 SIA sing 382 n n C7 C8 SIA sing 383 n n C7 O7 SIA sing 384 n n C7 H7 SIA sing 385 n n C8 C9 SIA sing 386 n n C8 O8 SIA sing 387 n n C8 H8 SIA sing 388 n n C9 O9 SIA sing 389 n n C9 H92 SIA sing 390 n n C9 H91 SIA sing 391 n n C10 C11 SIA sing 392 n n C10 N5 SIA sing 393 n n C10 O10 SIA doub 394 n n C11 H111 SIA sing 395 n n C11 H113 SIA sing 396 n n C11 H112 SIA sing 397 n n N5 HN5 SIA sing 398 n n O1B HO1B SIA sing 399 n n O2 HO2 SIA sing 400 n n O4 HO4 SIA sing 401 n n O7 HO7 SIA sing 402 n n O8 HO8 SIA sing 403 n n O9 HO9 SIA sing 404 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 SIA DNeup5Aca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 SIA 'N-acetyl-a-D-neuraminic acid' 'COMMON NAME' GMML 1 SIA a-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 SIA Neu5Ac 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4WRL _atom_sites.fract_transf_matrix[1][1] 0.006993 _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] 0.006993 _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] 0.007229 _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 J 6 SIA A 1 407 407 SIA SIA . K 7 NAG A 1 408 408 NAG NAG . L 7 NAG C 1 405 405 NAG NAG . M 7 NAG C 1 406 406 NAG NAG . # 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 SIA . . . J 6 -1.763 -0.98 -56.487 1 217.2 ? C1 SIA 407 A 1 HETATM 2 C C2 SIA . . . J 6 -3.227 -1.271 -56.704 1 208.54 ? C2 SIA 407 A 1 HETATM 3 C C3 SIA . . . J 6 -4.053 -0.024 -56.412 1 202.67 ? C3 SIA 407 A 1 HETATM 4 C C4 SIA . . . J 6 -3.787 1.068 -57.441 1 199.22 ? C4 SIA 407 A 1 HETATM 5 C C5 SIA . . . J 6 -3.903 0.517 -58.857 1 202.08 ? C5 SIA 407 A 1 HETATM 6 C C6 SIA . . . J 6 -3.062 -0.743 -59.018 1 205.46 ? C6 SIA 407 A 1 HETATM 7 C C7 SIA . . . J 6 -3.227 -1.334 -60.413 1 208.08 ? C7 SIA 407 A 1 HETATM 8 C C8 SIA . . . J 6 -1.926 -1.241 -61.202 1 206.51 ? C8 SIA 407 A 1 HETATM 9 C C9 SIA . . . J 6 -0.855 -2.14 -60.597 1 203.08 ? C9 SIA 407 A 1 HETATM 10 C C10 SIA . . . J 6 -4.261 1.877 -60.834 1 189.45 ? C10 SIA 407 A 1 HETATM 11 C C11 SIA . . . J 6 -3.734 2.985 -61.697 1 182.94 ? C11 SIA 407 A 1 HETATM 12 N N5 SIA . . . J 6 -3.483 1.52 -59.815 1 195.83 ? N5 SIA 407 A 1 HETATM 13 O O1A SIA . . . J 6 -0.933 -1.472 -57.282 1 221.35 ? O1A SIA 407 A 1 HETATM 14 O O1B SIA . . . J 6 -1.435 -0.257 -55.522 1 218.46 ? O1B SIA 407 A 1 HETATM 15 O O4 SIA . . . J 6 -4.729 2.132 -57.263 1 193.93 ? O4 SIA 407 A 1 HETATM 16 O O6 SIA . . . J 6 -3.454 -1.71 -58.044 1 206.27 ? O6 SIA 407 A 1 HETATM 17 O O7 SIA . . . J 6 -3.624 -2.705 -60.307 1 206.8 ? O7 SIA 407 A 1 HETATM 18 O O8 SIA . . . J 6 -2.163 -1.63 -62.56 1 204.15 ? O8 SIA 407 A 1 HETATM 19 O O9 SIA . . . J 6 0.432 -1.54 -60.782 1 198.37 ? O9 SIA 407 A 1 HETATM 20 O O10 SIA . . . J 6 -5.333 1.337 -61.053 1 190.17 ? O10 SIA 407 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 378 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #