data_2YI1 # _model_server_result.job_id RcNbghTavBYPYwsBLZf4ZA _model_server_result.datetime_utc '2024-11-05 08:06:34' _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 2yi1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 2YI1 # _exptl.entry_id 2YI1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-D-mannopyranose _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 2YI1 _cell.length_a 90.7 _cell.length_b 90.7 _cell.length_c 101.49 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YI1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_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,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 36 A ASP 413 1_555 D MG MG . A MG 1717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc2 A OD1 ASN 139 A ASN 516 1_555 F CA CA . A CA 1719 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.519 ? metalc ? metalc3 A O GLY 171 A GLY 548 1_555 F CA CA . A CA 1719 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.505 ? metalc ? metalc4 A O ALA 187 A ALA 564 1_555 F CA CA . A CA 1719 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.789 ? metalc ? metalc5 A O ALA 188 A ALA 565 1_555 F CA CA . A CA 1719 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.568 ? metalc ? metalc6 A ND1 HIS 192 A HIS 569 1_555 O ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 A SG CYS 202 A CYS 579 1_555 O ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc8 A SG CYS 204 A CYS 581 1_555 O ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc9 A SG CYS 209 A CYS 586 1_555 O ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc10 D MG MG . A MG 1717 1_555 N O1B ADP . A ADP 1727 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc11 D MG MG . A MG 1717 1_555 P O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc12 D MG MG . A MG 1717 1_555 P O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc13 D MG MG . A MG 1717 1_555 P O HOH . A HOH 2142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc14 F CA CA . A CA 1719 1_555 P O HOH . A HOH 2046 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc15 F CA CA . A CA 1719 1_555 P O HOH . A HOH 2066 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.526 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id BM3 _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-mannosamine;2-acetamido-2-deoxy-alpha-D-mannose;2-acetamido-2-deoxy-D-mannose;2-acetamido-2-deoxy-mannose;2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE # 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 O1 BM3 sing 185 n n C1 C2 BM3 sing 186 n n C1 O5 BM3 sing 187 n n C1 H1 BM3 sing 188 n n O1 HO1 BM3 sing 189 n n C2 N2 BM3 sing 190 n n C2 C3 BM3 sing 191 n n C2 H2 BM3 sing 192 n n N2 C7 BM3 sing 193 n n N2 HN2 BM3 sing 194 n n C7 O7 BM3 doub 195 n n C7 C8 BM3 sing 196 n n C8 H81 BM3 sing 197 n n C8 H82 BM3 sing 198 n n C8 H83 BM3 sing 199 n n C3 O3 BM3 sing 200 n n C3 C4 BM3 sing 201 n n C3 H3 BM3 sing 202 n n O3 HO3 BM3 sing 203 n n C4 O4 BM3 sing 204 n n C4 C5 BM3 sing 205 n n C4 H4 BM3 sing 206 n n O4 HO4 BM3 sing 207 n n C5 C6 BM3 sing 208 n n C5 O5 BM3 sing 209 n n C5 H5 BM3 sing 210 n n C6 O6 BM3 sing 211 n n C6 H61 BM3 sing 212 n n C6 H62 BM3 sing 213 n n O6 HO6 BM3 sing 214 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 BM3 DManpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BM3 N-acetyl-a-D-mannopyranosamine 'COMMON NAME' GMML 1 BM3 a-D-ManpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BM3 ManNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2YI1 _atom_sites.fract_transf_matrix[1][1] 0.011025 _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] 0.011025 _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] 0.009853 _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 BMX A 1 1000 1000 BMX BMX . C 3 BM3 A 1 1001 1001 BM3 BM3 . D 4 MG A 1 1717 1717 MG MG . E 5 CA A 1 1718 1718 CA CA . F 5 CA A 1 1719 1719 CA CA . G 6 2PE A 1 1720 1720 2PE 2PE . H 7 PG4 A 1 1721 1721 PG4 PG4 . I 8 EDO A 1 1722 1722 EDO EDO . J 8 EDO A 1 1723 1723 EDO EDO . K 8 EDO A 1 1724 1724 EDO EDO . L 8 EDO A 1 1725 1725 EDO EDO . M 9 ACT A 1 1726 1726 ACT ACT . N 10 ADP A 1 1727 1727 ADP ADP . O 11 ZN A 1 2000 2000 ZN ZN . P 12 HOH A 1 2001 2001 HOH HOH . P 12 HOH A 2 2002 2002 HOH HOH . P 12 HOH A 3 2003 2003 HOH HOH . P 12 HOH A 4 2004 2004 HOH HOH . P 12 HOH A 5 2005 2005 HOH HOH . P 12 HOH A 6 2006 2006 HOH HOH . P 12 HOH A 7 2007 2007 HOH HOH . P 12 HOH A 8 2008 2008 HOH HOH . P 12 HOH A 9 2009 2009 HOH HOH . P 12 HOH A 10 2010 2010 HOH HOH . P 12 HOH A 11 2011 2011 HOH HOH . P 12 HOH A 12 2012 2012 HOH HOH . P 12 HOH A 13 2013 2013 HOH HOH . P 12 HOH A 14 2014 2014 HOH HOH . P 12 HOH A 15 2015 2015 HOH HOH . P 12 HOH A 16 2016 2016 HOH HOH . P 12 HOH A 17 2017 2017 HOH HOH . P 12 HOH A 18 2018 2018 HOH HOH . P 12 HOH A 19 2019 2019 HOH HOH . P 12 HOH A 20 2020 2020 HOH HOH . P 12 HOH A 21 2021 2021 HOH HOH . P 12 HOH A 22 2022 2022 HOH HOH . P 12 HOH A 23 2023 2023 HOH HOH . P 12 HOH A 24 2024 2024 HOH HOH . P 12 HOH A 25 2025 2025 HOH HOH . P 12 HOH A 26 2026 2026 HOH HOH . P 12 HOH A 27 2027 2027 HOH HOH . P 12 HOH A 28 2028 2028 HOH HOH . P 12 HOH A 29 2029 2029 HOH HOH . P 12 HOH A 30 2030 2030 HOH HOH . P 12 HOH A 31 2031 2031 HOH HOH . P 12 HOH A 32 2032 2032 HOH HOH . P 12 HOH A 33 2033 2033 HOH HOH . P 12 HOH A 34 2034 2034 HOH HOH . P 12 HOH A 35 2035 2035 HOH HOH . P 12 HOH A 36 2036 2036 HOH HOH . P 12 HOH A 37 2037 2037 HOH HOH . P 12 HOH A 38 2038 2038 HOH HOH . P 12 HOH A 39 2039 2039 HOH HOH . P 12 HOH A 40 2040 2040 HOH HOH . P 12 HOH A 41 2041 2041 HOH HOH . P 12 HOH A 42 2042 2042 HOH HOH . P 12 HOH A 43 2043 2043 HOH HOH . P 12 HOH A 44 2044 2044 HOH HOH . P 12 HOH A 45 2045 2045 HOH HOH . P 12 HOH A 46 2046 2046 HOH HOH . P 12 HOH A 47 2047 2047 HOH HOH . P 12 HOH A 48 2048 2048 HOH HOH . P 12 HOH A 49 2049 2049 HOH HOH . P 12 HOH A 50 2050 2050 HOH HOH . P 12 HOH A 51 2051 2051 HOH HOH . P 12 HOH A 52 2052 2052 HOH HOH . P 12 HOH A 53 2053 2053 HOH HOH . P 12 HOH A 54 2054 2054 HOH HOH . P 12 HOH A 55 2055 2055 HOH HOH . P 12 HOH A 56 2056 2056 HOH HOH . P 12 HOH A 57 2057 2057 HOH HOH . P 12 HOH A 58 2058 2058 HOH HOH . P 12 HOH A 59 2059 2059 HOH HOH . P 12 HOH A 60 2060 2060 HOH HOH . P 12 HOH A 61 2061 2061 HOH HOH . P 12 HOH A 62 2062 2062 HOH HOH . P 12 HOH A 63 2063 2063 HOH HOH . P 12 HOH A 64 2064 2064 HOH HOH . P 12 HOH A 65 2065 2065 HOH HOH . P 12 HOH A 66 2066 2066 HOH HOH . P 12 HOH A 67 2067 2067 HOH HOH . P 12 HOH A 68 2068 2068 HOH HOH . P 12 HOH A 69 2069 2069 HOH HOH . P 12 HOH A 70 2070 2070 HOH HOH . P 12 HOH A 71 2071 2071 HOH HOH . P 12 HOH A 72 2072 2072 HOH HOH . P 12 HOH A 73 2073 2073 HOH HOH . P 12 HOH A 74 2074 2074 HOH HOH . P 12 HOH A 75 2075 2075 HOH HOH . P 12 HOH A 76 2076 2076 HOH HOH . P 12 HOH A 77 2077 2077 HOH HOH . P 12 HOH A 78 2078 2078 HOH HOH . P 12 HOH A 79 2079 2079 HOH HOH . P 12 HOH A 80 2080 2080 HOH HOH . P 12 HOH A 81 2081 2081 HOH HOH . P 12 HOH A 82 2082 2082 HOH HOH . P 12 HOH A 83 2083 2083 HOH HOH . P 12 HOH A 84 2084 2084 HOH HOH . P 12 HOH A 85 2085 2085 HOH HOH . P 12 HOH A 86 2086 2086 HOH HOH . P 12 HOH A 87 2087 2087 HOH HOH . P 12 HOH A 88 2088 2088 HOH HOH . P 12 HOH A 89 2089 2089 HOH HOH . P 12 HOH A 90 2090 2090 HOH HOH . P 12 HOH A 91 2091 2091 HOH HOH . P 12 HOH A 92 2092 2092 HOH HOH . P 12 HOH A 93 2093 2093 HOH HOH . P 12 HOH A 94 2094 2094 HOH HOH . P 12 HOH A 95 2095 2095 HOH HOH . P 12 HOH A 96 2096 2096 HOH HOH . P 12 HOH A 97 2097 2097 HOH HOH . P 12 HOH A 98 2098 2098 HOH HOH . P 12 HOH A 99 2099 2099 HOH HOH . P 12 HOH A 100 2100 2100 HOH HOH . P 12 HOH A 101 2101 2101 HOH HOH . P 12 HOH A 102 2102 2102 HOH HOH . P 12 HOH A 103 2103 2103 HOH HOH . P 12 HOH A 104 2104 2104 HOH HOH . P 12 HOH A 105 2105 2105 HOH HOH . P 12 HOH A 106 2106 2106 HOH HOH . P 12 HOH A 107 2107 2107 HOH HOH . P 12 HOH A 108 2108 2108 HOH HOH . P 12 HOH A 109 2109 2109 HOH HOH . P 12 HOH A 110 2110 2110 HOH HOH . P 12 HOH A 111 2111 2111 HOH HOH . P 12 HOH A 112 2112 2112 HOH HOH . P 12 HOH A 113 2113 2113 HOH HOH . P 12 HOH A 114 2114 2114 HOH HOH . P 12 HOH A 115 2115 2115 HOH HOH . P 12 HOH A 116 2116 2116 HOH HOH . P 12 HOH A 117 2117 2117 HOH HOH . P 12 HOH A 118 2118 2118 HOH HOH . P 12 HOH A 119 2119 2119 HOH HOH . P 12 HOH A 120 2120 2120 HOH HOH . P 12 HOH A 121 2121 2121 HOH HOH . P 12 HOH A 122 2122 2122 HOH HOH . P 12 HOH A 123 2123 2123 HOH HOH . P 12 HOH A 124 2124 2124 HOH HOH . P 12 HOH A 125 2125 2125 HOH HOH . P 12 HOH A 126 2126 2126 HOH HOH . P 12 HOH A 127 2127 2127 HOH HOH . P 12 HOH A 128 2128 2128 HOH HOH . P 12 HOH A 129 2129 2129 HOH HOH . P 12 HOH A 130 2130 2130 HOH HOH . P 12 HOH A 131 2131 2131 HOH HOH . P 12 HOH A 132 2132 2132 HOH HOH . P 12 HOH A 133 2133 2133 HOH HOH . P 12 HOH A 134 2134 2134 HOH HOH . P 12 HOH A 135 2135 2135 HOH HOH . P 12 HOH A 136 2136 2136 HOH HOH . P 12 HOH A 137 2137 2137 HOH HOH . P 12 HOH A 138 2138 2138 HOH HOH . P 12 HOH A 139 2139 2139 HOH HOH . P 12 HOH A 140 2140 2140 HOH HOH . P 12 HOH A 141 2141 2141 HOH HOH . P 12 HOH A 142 2142 2142 HOH HOH . P 12 HOH A 143 2143 2143 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 BM3 . B . C 3 31.222 11.648 -7.941 0.6 19.15 ? C1 BM3 1001 A 1 HETATM 2 O O1 BM3 . B . C 3 30.698 12.679 -7.165 0.6 18.67 ? O1 BM3 1001 A 1 HETATM 3 C C2 BM3 . B . C 3 30.18 10.986 -8.813 0.6 19.33 ? C2 BM3 1001 A 1 HETATM 4 N N2 BM3 . B . C 3 30.938 10.084 -9.697 0.6 16.3 ? N2 BM3 1001 A 1 HETATM 5 C C7 BM3 . B . C 3 30.756 9.971 -11.112 0.6 17.28 ? C7 BM3 1001 A 1 HETATM 6 O O7 BM3 . B . C 3 29.912 10.639 -11.708 0.6 21.76 ? O7 BM3 1001 A 1 HETATM 7 C C8 BM3 . B . C 3 31.625 8.996 -11.852 0.6 17.37 ? C8 BM3 1001 A 1 HETATM 8 C C3 BM3 . B . C 3 29.177 10.251 -8.018 0.6 17.09 ? C3 BM3 1001 A 1 HETATM 9 O O3 BM3 . B . C 3 28.216 9.633 -8.926 0.6 18.06 ? O3 BM3 1001 A 1 HETATM 10 C C4 BM3 . B . C 3 29.817 9.281 -7.163 0.6 18.88 ? C4 BM3 1001 A 1 HETATM 11 O O4 BM3 . B . C 3 28.832 8.677 -6.277 0.6 18.33 ? O4 BM3 1001 A 1 HETATM 12 C C5 BM3 . B . C 3 30.853 9.939 -6.297 0.6 19.36 ? C5 BM3 1001 A 1 HETATM 13 C C6 BM3 . B . C 3 31.577 9.001 -5.388 0.6 20.27 ? C6 BM3 1001 A 1 HETATM 14 O O6 BM3 . B . C 3 32.135 7.872 -6.044 0.6 19.76 ? O6 BM3 1001 A 1 HETATM 15 O O5 BM3 . B . C 3 31.806 10.675 -7.133 0.6 19.29 ? O5 BM3 1001 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #