data_4N5K # _model_server_result.job_id 296u3Tpb4HjZzrO05FN_fw _model_server_result.datetime_utc '2024-10-18 00:23:49' _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 4n5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 4N5K # _exptl.entry_id 4N5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.27 _entity.id 6 _entity.src_method man _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 4N5K _cell.length_a 154.698 _cell.length_b 154.698 _cell.length_c 154.698 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,K,L 1 1,2,3 C,D,I,J,M 2 1,4,5 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_544 -z,x-1/2,-y-1/2 0 0 -1 1 0 0 0 -1 0 0 -77.349 -77.349 3 'crystal symmetry operation' 11_545 y+1/2,-z-1/2,-x 0 1 0 0 0 -1 -1 0 0 77.349 -77.349 0 4 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 5 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _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 # 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 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 521 NAG 3 n E NAG 2 E 2 NAG A 522 NAG 3 n E BMA 3 E 3 BMA A 523 BMA 4 n F GAL 1 F 1 GAL X 102 GAL 4 n F SIA 2 F 2 SIA X 101 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 4 A CYS 14 1_555 B SG CYS 134 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 268 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 54 A CYS 64 1_555 A SG CYS 66 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 87 A CYS 97 1_555 A SG CYS 129 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 272 A CYS 281 1_555 A SG CYS 296 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf6 B SG CYS 141 B CYS 144 1_555 B SG CYS 145 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 4 C CYS 14 1_555 D SG CYS 134 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 42 C CYS 52 1_555 C SG CYS 268 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 C SG CYS 54 C CYS 64 1_555 C SG CYS 66 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf10 C SG CYS 87 C CYS 97 1_555 C SG CYS 129 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 C SG CYS 272 C CYS 281 1_555 C SG CYS 296 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf12 D SG CYS 141 D CYS 144 1_555 D SG CYS 145 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 28 A ASN 38 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 231 A ASN 240 1_555 G C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B ND2 ASN 79 B ASN 82 1_555 H C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 D ND2 ASN 79 D ASN 82 1_555 J C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 F O3 GAL . F GAL 1 1_555 F C2 SIA . F SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 ? # 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 4N5K _atom_sites.fract_transf_matrix[1][1] 0.006464 _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] 0.006464 _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] 0.006464 _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 G 5 NAG A 1 404 531 NAG NAG . H 5 NAG B 1 201 541 NAG NAG . I 6 SIA C 1 401 201 SIA SIA . J 5 NAG D 1 201 541 NAG NAG . K 7 HOH A 1 501 3 HOH HOH . K 7 HOH A 2 502 5 HOH HOH . K 7 HOH A 3 503 6 HOH HOH . K 7 HOH A 4 504 12 HOH HOH . K 7 HOH A 5 505 16 HOH HOH . K 7 HOH A 6 506 17 HOH HOH . K 7 HOH A 7 507 19 HOH HOH . K 7 HOH A 8 508 22 HOH HOH . K 7 HOH A 9 509 23 HOH HOH . K 7 HOH A 10 510 24 HOH HOH . K 7 HOH A 11 511 25 HOH HOH . K 7 HOH A 12 512 31 HOH HOH . K 7 HOH A 13 513 32 HOH HOH . K 7 HOH A 14 514 33 HOH HOH . K 7 HOH A 15 515 35 HOH HOH . L 7 HOH B 1 301 1 HOH HOH . L 7 HOH B 2 302 2 HOH HOH . L 7 HOH B 3 303 4 HOH HOH . L 7 HOH B 4 304 7 HOH HOH . L 7 HOH B 5 305 9 HOH HOH . L 7 HOH B 6 306 10 HOH HOH . L 7 HOH B 7 307 13 HOH HOH . L 7 HOH B 8 308 14 HOH HOH . L 7 HOH B 9 309 20 HOH HOH . L 7 HOH B 10 310 21 HOH HOH . L 7 HOH B 11 311 29 HOH HOH . L 7 HOH B 12 312 30 HOH HOH . M 7 HOH C 1 501 8 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 SIA . . . I 6 16.385 -8.364 30.134 1 131.4 ? C1 SIA 401 C 1 HETATM 2 C C2 SIA . . . I 6 17.331 -7.21 29.913 1 128.49 ? C2 SIA 401 C 1 HETATM 3 C C3 SIA . . . I 6 18.674 -7.519 30.564 1 126.77 ? C3 SIA 401 C 1 HETATM 4 C C4 SIA . . . I 6 19.775 -7.615 29.516 1 124.42 ? C4 SIA 401 C 1 HETATM 5 C C5 SIA . . . I 6 19.841 -6.341 28.686 1 122.62 ? C5 SIA 401 C 1 HETATM 6 C C6 SIA . . . I 6 18.462 -6.025 28.105 1 124.32 ? C6 SIA 401 C 1 HETATM 7 C C7 SIA . . . I 6 17.991 -4.595 28.407 1 122.46 ? C7 SIA 401 C 1 HETATM 8 C C8 SIA . . . I 6 16.573 -4.337 27.899 1 119.67 ? C8 SIA 401 C 1 HETATM 9 C C9 SIA . . . I 6 16.573 -3.355 26.735 1 115.9 ? C9 SIA 401 C 1 HETATM 10 C C10 SIA . . . I 6 21.287 -5.525 26.864 1 115.86 ? C10 SIA 401 C 1 HETATM 11 C C11 SIA . . . I 6 22.289 -5.933 25.825 1 115.12 ? C11 SIA 401 C 1 HETATM 12 N N5 SIA . . . I 6 20.818 -6.514 27.625 1 119.24 ? N5 SIA 401 C 1 HETATM 13 O O1A SIA . . . I 6 15.914 -8.947 29.134 1 132.11 ? O1A SIA 401 C 1 HETATM 14 O O1B SIA . . . I 6 16.106 -8.698 31.307 1 132.65 ? O1B SIA 401 C 1 HETATM 15 O O4 SIA . . . I 6 21.033 -7.853 30.159 1 124.07 ? O4 SIA 401 C 1 HETATM 16 O O6 SIA . . . I 6 17.492 -7.009 28.505 1 126.98 ? O6 SIA 401 C 1 HETATM 17 O O7 SIA . . . I 6 18.063 -4.29 29.807 1 122.65 ? O7 SIA 401 C 1 HETATM 18 O O8 SIA . . . I 6 15.983 -5.569 27.474 1 119.86 ? O8 SIA 401 C 1 HETATM 19 O O9 SIA . . . I 6 15.242 -2.891 26.493 1 113.23 ? O9 SIA 401 C 1 HETATM 20 O O10 SIA . . . I 6 20.94 -4.364 26.993 1 113.72 ? O10 SIA 401 C 1 # _model_server_stats.io_time_ms 111 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #