data_2YD8 # _model_server_result.job_id QZ1w3dVB5GswSKfHaf5Kiw _model_server_result.datetime_utc '2024-11-25 08:09:02' _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 2yd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1228}' # _entry.id 2YD8 # _exptl.entry_id 2YD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 500.409 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose _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 120 _cell.entry_id 2YD8 _cell.length_a 78.768 _cell.length_b 78.768 _cell.length_c 71.907 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 A SG CYS 28 A CYS 54 1_555 A SG CYS 81 A CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf2 A SG CYS 130 A CYS 156 1_555 A SG CYS 181 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C6 H12 O18 S4' _chem_comp.formula_weight 500.409 _chem_comp.id YYJ _chem_comp.mon_nstd_flag n _chem_comp.name 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms ? # 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 YYJ sing 376 n n C1 O1 YYJ sing 377 n n C1 H11 YYJ sing 378 n n C1 H12 YYJ sing 379 n n C2 C3 YYJ sing 380 n n C2 O2 YYJ sing 381 n n C2 O5 YYJ sing 382 n n C3 C4 YYJ sing 383 n n C3 O3 YYJ sing 384 n n C3 H3 YYJ sing 385 n n C4 C5 YYJ sing 386 n n C4 O4 YYJ sing 387 n n C4 H4 YYJ sing 388 n n C5 C6 YYJ sing 389 n n C5 O5 YYJ sing 390 n n C5 H5 YYJ sing 391 n n C6 O6 YYJ sing 392 n n C6 H61 YYJ sing 393 n n C6 H62 YYJ sing 394 n n O1 S1 YYJ sing 395 n n O1S1 S1 YYJ sing 396 n n O1S1 H1S1 YYJ sing 397 n n O1S3 H1S3 YYJ sing 398 n n O1S3 S3 YYJ sing 399 n n O1S4 S4 YYJ sing 400 n n O1S4 H1S4 YYJ sing 401 n n O1S6 H1S6 YYJ sing 402 n n O1S6 S6 YYJ sing 403 n n O2 HO2 YYJ sing 404 n n O2S1 S1 YYJ doub 405 n n O2S3 S3 YYJ doub 406 n n O2S4 S4 YYJ doub 407 n n O2S6 S6 YYJ doub 408 n n O3 S3 YYJ sing 409 n n O3S1 S1 YYJ doub 410 n n O3S3 S3 YYJ doub 411 n n O3S4 S4 YYJ doub 412 n n O3S6 S6 YYJ doub 413 n n O4 S4 YYJ sing 414 n n O6 S6 YYJ sing 415 n n # _atom_sites.entry_id 2YD8 _atom_sites.fract_transf_matrix[1][1] 0.012696 _atom_sites.fract_transf_matrix[1][2] 0.00733 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01466 _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] 0.013907 _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 B 2 YYJ A 1 1228 1228 YYJ SCR . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 HOH HOH . C 3 HOH A 61 2061 2061 HOH HOH . C 3 HOH A 62 2062 2062 HOH HOH . C 3 HOH A 63 2063 2063 HOH HOH . C 3 HOH A 64 2064 2064 HOH HOH . C 3 HOH A 65 2065 2065 HOH HOH . C 3 HOH A 66 2066 2066 HOH HOH . C 3 HOH A 67 2067 2067 HOH HOH . C 3 HOH A 68 2068 2068 HOH HOH . C 3 HOH A 69 2069 2069 HOH HOH . C 3 HOH A 70 2070 2070 HOH HOH . C 3 HOH A 71 2071 2071 HOH HOH . C 3 HOH A 72 2072 2072 HOH HOH . C 3 HOH A 73 2073 2073 HOH HOH . C 3 HOH A 74 2074 2074 HOH HOH . C 3 HOH A 75 2075 2075 HOH HOH . C 3 HOH A 76 2076 2076 HOH HOH . C 3 HOH A 77 2077 2077 HOH HOH . C 3 HOH A 78 2078 2078 HOH HOH . C 3 HOH A 79 2079 2079 HOH HOH . C 3 HOH A 80 2080 2080 HOH HOH . C 3 HOH A 81 2081 2081 HOH HOH . C 3 HOH A 82 2082 2082 HOH HOH . C 3 HOH A 83 2083 2083 HOH HOH . C 3 HOH A 84 2084 2084 HOH HOH . C 3 HOH A 85 2085 2085 HOH HOH . C 3 HOH A 86 2086 2086 HOH HOH . C 3 HOH A 87 2087 2087 HOH HOH . C 3 HOH A 88 2088 2088 HOH HOH . C 3 HOH A 89 2089 2089 HOH HOH . C 3 HOH A 90 2090 2090 HOH HOH . C 3 HOH A 91 2091 2091 HOH HOH . C 3 HOH A 92 2092 2092 HOH HOH . C 3 HOH A 93 2093 2093 HOH HOH . C 3 HOH A 94 2094 2094 HOH HOH . C 3 HOH A 95 2095 2095 HOH HOH . C 3 HOH A 96 2096 2096 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 YYJ . . . B 2 -50.895 14.764 10.19 1 160.25 ? C1 YYJ 1228 A 1 HETATM 2 C C2 YYJ . . . B 2 -50.261 15.25 8.874 1 155.02 ? C2 YYJ 1228 A 1 HETATM 3 C C3 YYJ . . . B 2 -48.912 14.665 8.576 1 153.54 ? C3 YYJ 1228 A 1 HETATM 4 C C4 YYJ . . . B 2 -48.025 15.747 8.646 1 147.45 ? C4 YYJ 1228 A 1 HETATM 5 C C5 YYJ . . . B 2 -48.793 16.77 9.396 1 146.99 ? C5 YYJ 1228 A 1 HETATM 6 C C6 YYJ . . . B 2 -48.311 18.15 9.168 1 142.22 ? C6 YYJ 1228 A 1 HETATM 7 O O1 YYJ . . . B 2 -51.654 15.729 10.895 1 167.05 ? O1 YYJ 1228 A 1 HETATM 8 O O1S1 YYJ . . . B 2 -50.201 15.56 12.83 1 173.93 ? O1S1 YYJ 1228 A 1 HETATM 9 O O1S3 YYJ . . . B 2 -48.878 12.324 5.646 1 155.8 ? O1S3 YYJ 1228 A 1 HETATM 10 O O1S4 YYJ . . . B 2 -44.519 15.239 9.106 1 132.9 ? O1S4 YYJ 1228 A 1 HETATM 11 O O1S6 YYJ . . . B 2 -47.895 20.651 11.557 1 135.33 ? O1S6 YYJ 1228 A 1 HETATM 12 O O2 YYJ . . . B 2 -51.135 14.997 7.845 1 156.18 ? O2 YYJ 1228 A 1 HETATM 13 O O2S1 YYJ . . . B 2 -51.939 17.18 12.821 1 173.58 ? O2S1 YYJ 1228 A 1 HETATM 14 O O2S3 YYJ . . . B 2 -47.435 12.113 7.52 1 156.33 ? O2S3 YYJ 1228 A 1 HETATM 15 O O2S4 YYJ . . . B 2 -45.701 17.188 8.326 1 128.59 ? O2S4 YYJ 1228 A 1 HETATM 16 O O2S6 YYJ . . . B 2 -49.597 18.984 11.355 1 136.83 ? O2S6 YYJ 1228 A 1 HETATM 17 O O3 YYJ . . . B 2 -48.868 14.086 7.281 1 157.28 ? O3 YYJ 1228 A 1 HETATM 18 O O3S1 YYJ . . . B 2 -52.472 14.864 13.017 1 174.66 ? O3S1 YYJ 1228 A 1 HETATM 19 O O3S3 YYJ . . . B 2 -49.822 11.899 7.801 1 159 ? O3S3 YYJ 1228 A 1 HETATM 20 O O3S4 YYJ . . . B 2 -45.492 16.748 10.687 1 133.2 ? O3S4 YYJ 1228 A 1 HETATM 21 O O3S6 YYJ . . . B 2 -47.586 18.492 12.571 1 133.19 ? O3S6 YYJ 1228 A 1 HETATM 22 O O4 YYJ . . . B 2 -46.884 15.354 9.364 1 141.1 ? O4 YYJ 1228 A 1 HETATM 23 O O5 YYJ . . . B 2 -50.074 16.629 8.917 1 150.68 ? O5 YYJ 1228 A 1 HETATM 24 O O6 YYJ . . . B 2 -47.514 18.714 10.176 1 137.23 ? O6 YYJ 1228 A 1 HETATM 25 S S1 YYJ . . . B 2 -51.563 15.829 12.4 1 173.29 ? S1 YYJ 1228 A 1 HETATM 26 S S3 YYJ . . . B 2 -48.749 12.603 7.061 1 157.88 ? S3 YYJ 1228 A 1 HETATM 27 S S4 YYJ . . . B 2 -45.653 16.131 9.358 1 133.22 ? S4 YYJ 1228 A 1 HETATM 28 S S6 YYJ . . . B 2 -48.144 19.213 11.41 1 135.01 ? S6 YYJ 1228 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #