data_2YB5 # _model_server_result.job_id GPlSkBxXEs_b17oWs4tUow _model_server_result.datetime_utc '2024-12-22 06:30:57' _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 2yb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1217}' # _entry.id 2YB5 # _exptl.entry_id 2YB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.72 _cell.angle_gamma 90 _cell.entry_id 2YB5 _cell.length_a 34.15 _cell.length_b 109.61 _cell.length_c 61.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,M 1 1 B,D,E,F,G,H,I,J,K,L,N 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 L N 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 SG CYS 158 A CYS 155 1_555 C ZN ZN . A ZN 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A SG CYS 161 A CYS 158 1_555 C ZN ZN . A ZN 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 A SG CYS 191 A CYS 188 1_555 C ZN ZN . A ZN 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 A SG CYS 197 A CYS 194 1_555 C ZN ZN . A ZN 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc5 B SG CYS 158 F CYS 155 1_555 K ZN ZN . F ZN 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc6 B SG CYS 161 F CYS 158 1_555 K ZN ZN . F ZN 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 B SG CYS 191 F CYS 188 1_555 K ZN ZN . F ZN 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc8 B SG CYS 197 F CYS 194 1_555 K ZN ZN . F ZN 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 EDO sing 83 n n C1 C2 EDO sing 84 n n C1 H11 EDO sing 85 n n C1 H12 EDO sing 86 n n O1 HO1 EDO sing 87 n n C2 O2 EDO sing 88 n n C2 H21 EDO sing 89 n n C2 H22 EDO sing 90 n n O2 HO2 EDO sing 91 n n # _atom_sites.entry_id 2YB5 _atom_sites.fract_transf_matrix[1][1] 0.029283 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006075 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009123 _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] 0.016701 _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 2 ZN A 1 1213 1213 ZN ZN . D 3 EDO F 1 1213 1213 EDO EDO . E 3 EDO F 1 1214 1214 EDO EDO . F 3 EDO F 1 1215 1215 EDO EDO . G 3 EDO F 1 1216 1216 EDO EDO . H 3 EDO F 1 1217 1217 EDO EDO . I 3 EDO F 1 1218 1218 EDO EDO . J 3 EDO F 1 1219 1219 EDO EDO . K 2 ZN F 1 1220 1220 ZN ZN . L 3 EDO F 1 1221 1221 EDO EDO . M 4 HOH A 1 2001 2001 HOH HOH . M 4 HOH A 2 2002 2002 HOH HOH . M 4 HOH A 3 2003 2003 HOH HOH . M 4 HOH A 4 2004 2004 HOH HOH . M 4 HOH A 5 2005 2005 HOH HOH . M 4 HOH A 6 2006 2006 HOH HOH . M 4 HOH A 7 2007 2007 HOH HOH . M 4 HOH A 8 2008 2008 HOH HOH . M 4 HOH A 9 2009 2009 HOH HOH . M 4 HOH A 10 2010 2010 HOH HOH . M 4 HOH A 11 2011 2011 HOH HOH . M 4 HOH A 12 2012 2012 HOH HOH . M 4 HOH A 13 2013 2013 HOH HOH . M 4 HOH A 14 2014 2014 HOH HOH . M 4 HOH A 15 2015 2015 HOH HOH . M 4 HOH A 16 2016 2016 HOH HOH . M 4 HOH A 17 2017 2017 HOH HOH . M 4 HOH A 18 2018 2018 HOH HOH . M 4 HOH A 19 2019 2019 HOH HOH . M 4 HOH A 20 2020 2020 HOH HOH . M 4 HOH A 21 2021 2021 HOH HOH . M 4 HOH A 22 2022 2022 HOH HOH . M 4 HOH A 23 2023 2023 HOH HOH . M 4 HOH A 24 2024 2024 HOH HOH . M 4 HOH A 25 2025 2025 HOH HOH . M 4 HOH A 26 2026 2026 HOH HOH . M 4 HOH A 27 2027 2027 HOH HOH . M 4 HOH A 28 2028 2028 HOH HOH . M 4 HOH A 29 2029 2029 HOH HOH . M 4 HOH A 30 2030 2030 HOH HOH . M 4 HOH A 31 2031 2031 HOH HOH . M 4 HOH A 32 2032 2032 HOH HOH . M 4 HOH A 33 2033 2033 HOH HOH . M 4 HOH A 34 2034 2034 HOH HOH . M 4 HOH A 35 2035 2035 HOH HOH . M 4 HOH A 36 2036 2036 HOH HOH . M 4 HOH A 37 2037 2037 HOH HOH . M 4 HOH A 38 2038 2038 HOH HOH . M 4 HOH A 39 2039 2039 HOH HOH . M 4 HOH A 40 2040 2040 HOH HOH . M 4 HOH A 41 2041 2041 HOH HOH . M 4 HOH A 42 2042 2042 HOH HOH . M 4 HOH A 43 2043 2043 HOH HOH . M 4 HOH A 44 2044 2044 HOH HOH . M 4 HOH A 45 2045 2045 HOH HOH . M 4 HOH A 46 2046 2046 HOH HOH . M 4 HOH A 47 2047 2047 HOH HOH . M 4 HOH A 48 2048 2048 HOH HOH . M 4 HOH A 49 2049 2049 HOH HOH . M 4 HOH A 50 2050 2050 HOH HOH . M 4 HOH A 51 2051 2051 HOH HOH . M 4 HOH A 52 2052 2052 HOH HOH . M 4 HOH A 53 2053 2053 HOH HOH . M 4 HOH A 54 2054 2054 HOH HOH . M 4 HOH A 55 2055 2055 HOH HOH . M 4 HOH A 56 2056 2056 HOH HOH . M 4 HOH A 57 2057 2057 HOH HOH . M 4 HOH A 58 2058 2058 HOH HOH . M 4 HOH A 59 2059 2059 HOH HOH . M 4 HOH A 60 2060 2060 HOH HOH . M 4 HOH A 61 2061 2061 HOH HOH . M 4 HOH A 62 2062 2062 HOH HOH . M 4 HOH A 63 2063 2063 HOH HOH . M 4 HOH A 64 2064 2064 HOH HOH . M 4 HOH A 65 2065 2065 HOH HOH . M 4 HOH A 66 2066 2066 HOH HOH . M 4 HOH A 67 2067 2067 HOH HOH . M 4 HOH A 68 2068 2068 HOH HOH . M 4 HOH A 69 2069 2069 HOH HOH . M 4 HOH A 70 2070 2070 HOH HOH . M 4 HOH A 71 2071 2071 HOH HOH . M 4 HOH A 72 2072 2072 HOH HOH . M 4 HOH A 73 2073 2073 HOH HOH . M 4 HOH A 74 2074 2074 HOH HOH . M 4 HOH A 75 2075 2075 HOH HOH . M 4 HOH A 76 2076 2076 HOH HOH . M 4 HOH A 77 2077 2077 HOH HOH . M 4 HOH A 78 2078 2078 HOH HOH . M 4 HOH A 79 2079 2079 HOH HOH . M 4 HOH A 80 2080 2080 HOH HOH . M 4 HOH A 81 2081 2081 HOH HOH . M 4 HOH A 82 2082 2082 HOH HOH . M 4 HOH A 83 2083 2083 HOH HOH . M 4 HOH A 84 2084 2084 HOH HOH . M 4 HOH A 85 2085 2085 HOH HOH . M 4 HOH A 86 2086 2086 HOH HOH . M 4 HOH A 87 2087 2087 HOH HOH . M 4 HOH A 88 2088 2088 HOH HOH . M 4 HOH A 89 2089 2089 HOH HOH . M 4 HOH A 90 2090 2090 HOH HOH . M 4 HOH A 91 2091 2091 HOH HOH . N 4 HOH F 1 2001 2001 HOH HOH . N 4 HOH F 2 2002 2002 HOH HOH . N 4 HOH F 3 2003 2003 HOH HOH . N 4 HOH F 4 2004 2004 HOH HOH . N 4 HOH F 5 2005 2005 HOH HOH . N 4 HOH F 6 2006 2006 HOH HOH . N 4 HOH F 7 2007 2007 HOH HOH . N 4 HOH F 8 2008 2008 HOH HOH . N 4 HOH F 9 2009 2009 HOH HOH . N 4 HOH F 10 2010 2010 HOH HOH . N 4 HOH F 11 2011 2011 HOH HOH . N 4 HOH F 12 2012 2012 HOH HOH . N 4 HOH F 13 2013 2013 HOH HOH . N 4 HOH F 14 2014 2014 HOH HOH . N 4 HOH F 15 2015 2015 HOH HOH . N 4 HOH F 16 2016 2016 HOH HOH . N 4 HOH F 17 2017 2017 HOH HOH . N 4 HOH F 18 2018 2018 HOH HOH . N 4 HOH F 19 2019 2019 HOH HOH . N 4 HOH F 20 2020 2020 HOH HOH . N 4 HOH F 21 2021 2021 HOH HOH . N 4 HOH F 22 2022 2022 HOH HOH . N 4 HOH F 23 2023 2023 HOH HOH . N 4 HOH F 24 2024 2024 HOH HOH . N 4 HOH F 25 2025 2025 HOH HOH . N 4 HOH F 26 2026 2026 HOH HOH . N 4 HOH F 27 2027 2027 HOH HOH . N 4 HOH F 28 2028 2028 HOH HOH . N 4 HOH F 29 2029 2029 HOH HOH . N 4 HOH F 30 2030 2030 HOH HOH . N 4 HOH F 31 2031 2031 HOH HOH . N 4 HOH F 32 2032 2032 HOH HOH . N 4 HOH F 33 2033 2033 HOH HOH . N 4 HOH F 34 2034 2034 HOH HOH . N 4 HOH F 35 2035 2035 HOH HOH . N 4 HOH F 36 2036 2036 HOH HOH . N 4 HOH F 37 2037 2037 HOH HOH . N 4 HOH F 38 2038 2038 HOH HOH . N 4 HOH F 39 2039 2039 HOH HOH . N 4 HOH F 40 2040 2040 HOH HOH . N 4 HOH F 41 2041 2041 HOH HOH . N 4 HOH F 42 2042 2042 HOH HOH . N 4 HOH F 43 2043 2043 HOH HOH . N 4 HOH F 44 2044 2044 HOH HOH . N 4 HOH F 45 2045 2045 HOH HOH . N 4 HOH F 46 2046 2046 HOH HOH . N 4 HOH F 47 2047 2047 HOH HOH . N 4 HOH F 48 2048 2048 HOH HOH . N 4 HOH F 49 2049 2049 HOH HOH . N 4 HOH F 50 2050 2050 HOH HOH . N 4 HOH F 51 2051 2051 HOH HOH . N 4 HOH F 52 2052 2052 HOH HOH . N 4 HOH F 53 2053 2053 HOH HOH . N 4 HOH F 54 2054 2054 HOH HOH . N 4 HOH F 55 2055 2055 HOH HOH . N 4 HOH F 56 2056 2056 HOH HOH . N 4 HOH F 57 2057 2057 HOH HOH . N 4 HOH F 58 2058 2058 HOH HOH . N 4 HOH F 59 2059 2059 HOH HOH . N 4 HOH F 60 2060 2060 HOH HOH . N 4 HOH F 61 2061 2061 HOH HOH . N 4 HOH F 62 2062 2062 HOH HOH . N 4 HOH F 63 2063 2063 HOH HOH . N 4 HOH F 64 2064 2064 HOH HOH . N 4 HOH F 65 2065 2065 HOH HOH . N 4 HOH F 66 2066 2066 HOH HOH . N 4 HOH F 67 2067 2067 HOH HOH . N 4 HOH F 68 2068 2068 HOH HOH . N 4 HOH F 69 2069 2069 HOH HOH . N 4 HOH F 70 2070 2070 HOH HOH . N 4 HOH F 71 2071 2071 HOH HOH . N 4 HOH F 72 2072 2072 HOH HOH . N 4 HOH F 73 2073 2073 HOH HOH . N 4 HOH F 74 2074 2074 HOH HOH . N 4 HOH F 75 2075 2075 HOH HOH . N 4 HOH F 76 2076 2076 HOH HOH . N 4 HOH F 77 2077 2077 HOH HOH . N 4 HOH F 78 2078 2078 HOH HOH . N 4 HOH F 79 2079 2079 HOH HOH . N 4 HOH F 80 2080 2080 HOH HOH . N 4 HOH F 81 2081 2081 HOH HOH . N 4 HOH F 82 2082 2082 HOH HOH . N 4 HOH F 83 2083 2083 HOH HOH . N 4 HOH F 84 2084 2084 HOH HOH . N 4 HOH F 85 2085 2085 HOH HOH . N 4 HOH F 86 2086 2086 HOH HOH . N 4 HOH F 87 2087 2087 HOH HOH . N 4 HOH F 88 2088 2088 HOH HOH . N 4 HOH F 89 2089 2089 HOH HOH . N 4 HOH F 90 2090 2090 HOH HOH . N 4 HOH F 91 2091 2091 HOH HOH . N 4 HOH F 92 2092 2092 HOH HOH . N 4 HOH F 93 2093 2093 HOH HOH . N 4 HOH F 94 2094 2094 HOH HOH . N 4 HOH F 95 2095 2095 HOH HOH . N 4 HOH F 96 2096 2096 HOH HOH . N 4 HOH F 97 2097 2097 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 EDO . . . H 3 -9.144 6.778 13.307 1 54.21 ? C1 EDO 1217 F 1 HETATM 2 O O1 EDO . . . H 3 -8.068 6.527 12.386 1 52.89 ? O1 EDO 1217 F 1 HETATM 3 C C2 EDO . . . H 3 -8.923 6.057 14.641 1 53.65 ? C2 EDO 1217 F 1 HETATM 4 O O2 EDO . . . H 3 -8.394 6.968 15.615 1 54.35 ? O2 EDO 1217 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #