data_2YI1
#
_model_server_result.job_id            DfwDGcfz-Jzsvlseygxmtg 
_model_server_result.datetime_utc      '2024-11-21 16:42:18' 
_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":"L","auth_seq_id":1725}' 
#
_entry.id    2YI1 
#
_exptl.entry_id    2YI1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    4 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 8 I N N 
? 8 J N N 
? 8 K N N 
? 8 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 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           '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 263 n n 
C1 C2 EDO sing 264 n n 
C1 H11 EDO sing 265 n n 
C1 H12 EDO sing 266 n n 
O1 HO1 EDO sing 267 n n 
C2 O2 EDO sing 268 n n 
C2 H21 EDO sing 269 n n 
C2 H22 EDO sing 270 n n 
O2 HO2 EDO sing 271 n n 
#
_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 EDO . . . L 8 45.614 -1.54 -7.011 1 68.92 ? C1 EDO 1725 A 1 
HETATM 2 O O1 EDO . . . L 8 45.075 -1.035 -5.78 1 71.44 ? O1 EDO 1725 A 1 
HETATM 3 C C2 EDO . . . L 8 46.574 -2.678 -6.734 1 69.27 ? C2 EDO 1725 A 1 
HETATM 4 O O2 EDO . . . L 8 46.968 -3.289 -7.969 1 69.27 ? O2 EDO 1725 A 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           4 
#