data_5ZML
#
_model_server_result.job_id            gv1XL4f0Xu2PXVJdctCV-w 
_model_server_result.datetime_utc      '2024-11-19 16:39:43' 
_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          5zml 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":902}' 
#
_entry.id    5ZML 
#
_exptl.entry_id    5ZML 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    3 
_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            5ZML 
_cell.length_a            38.29 
_cell.length_b            91.61 
_cell.length_c            136.83 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZML 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F 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
covale ? covale1 B C ACE 1 B ACE 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale2 B C ARG 7 B ARG 7 1_555 B N MK8 8 B MK8 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale3 B C MK8 8 B MK8 8 1_555 B N GLN 9 B GLN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? 
covale ? covale4 B C LEU 11 B LEU 11 1_555 B N MK8 12 B MK8 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
covale ? covale5 B C MK8 12 B MK8 12 1_555 B N PHE 13 B PHE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.293 ? 
#
_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 89 n n 
C1 C2 EDO sing 90 n n 
C1 H11 EDO sing 91 n n 
C1 H12 EDO sing 92 n n 
O1 HO1 EDO sing 93 n n 
C2 O2 EDO sing 94 n n 
C2 H21 EDO sing 95 n n 
C2 H22 EDO sing 96 n n 
O2 HO2 EDO sing 97 n n 
#
_atom_sites.entry_id                     5ZML 
_atom_sites.fract_transf_matrix[1][1]    0.026116 
_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]    0.010916 
_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]    0.007308 
_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 3 NO3 A 1 901 901 NO3 NO3 . 
D 4 EDO A 1 902 902 EDO EDO . 
E 4 EDO A 1 903 903 EDO EDO . 
F 4 EDO A 1 904 1 EDO EDO . 
G 5 HOH A 1 1001 177 HOH HOH . 
G 5 HOH A 2 1002 117 HOH HOH . 
G 5 HOH A 3 1003 85 HOH HOH . 
G 5 HOH A 4 1004 181 HOH HOH . 
G 5 HOH A 5 1005 164 HOH HOH . 
G 5 HOH A 6 1006 6 HOH HOH . 
G 5 HOH A 7 1007 132 HOH HOH . 
G 5 HOH A 8 1008 25 HOH HOH . 
G 5 HOH A 9 1009 13 HOH HOH . 
G 5 HOH A 10 1010 99 HOH HOH . 
G 5 HOH A 11 1011 74 HOH HOH . 
G 5 HOH A 12 1012 41 HOH HOH . 
G 5 HOH A 13 1013 51 HOH HOH . 
G 5 HOH A 14 1014 7 HOH HOH . 
G 5 HOH A 15 1015 143 HOH HOH . 
G 5 HOH A 16 1016 145 HOH HOH . 
G 5 HOH A 17 1017 124 HOH HOH . 
G 5 HOH A 18 1018 35 HOH HOH . 
G 5 HOH A 19 1019 176 HOH HOH . 
G 5 HOH A 20 1020 183 HOH HOH . 
G 5 HOH A 21 1021 64 HOH HOH . 
G 5 HOH A 22 1022 166 HOH HOH . 
G 5 HOH A 23 1023 44 HOH HOH . 
G 5 HOH A 24 1024 173 HOH HOH . 
G 5 HOH A 25 1025 16 HOH HOH . 
G 5 HOH A 26 1026 125 HOH HOH . 
G 5 HOH A 27 1027 47 HOH HOH . 
G 5 HOH A 28 1028 15 HOH HOH . 
G 5 HOH A 29 1029 21 HOH HOH . 
G 5 HOH A 30 1030 168 HOH HOH . 
G 5 HOH A 31 1031 81 HOH HOH . 
G 5 HOH A 32 1032 104 HOH HOH . 
G 5 HOH A 33 1033 38 HOH HOH . 
G 5 HOH A 34 1034 22 HOH HOH . 
G 5 HOH A 35 1035 109 HOH HOH . 
G 5 HOH A 36 1036 83 HOH HOH . 
G 5 HOH A 37 1037 4 HOH HOH . 
G 5 HOH A 38 1038 197 HOH HOH . 
G 5 HOH A 39 1039 43 HOH HOH . 
G 5 HOH A 40 1040 169 HOH HOH . 
G 5 HOH A 41 1041 46 HOH HOH . 
G 5 HOH A 42 1042 34 HOH HOH . 
G 5 HOH A 43 1043 89 HOH HOH . 
G 5 HOH A 44 1044 114 HOH HOH . 
G 5 HOH A 45 1045 133 HOH HOH . 
G 5 HOH A 46 1046 3 HOH HOH . 
G 5 HOH A 47 1047 20 HOH HOH . 
G 5 HOH A 48 1048 79 HOH HOH . 
G 5 HOH A 49 1049 80 HOH HOH . 
G 5 HOH A 50 1050 162 HOH HOH . 
G 5 HOH A 51 1051 86 HOH HOH . 
G 5 HOH A 52 1052 96 HOH HOH . 
G 5 HOH A 53 1053 61 HOH HOH . 
G 5 HOH A 54 1054 48 HOH HOH . 
G 5 HOH A 55 1055 60 HOH HOH . 
G 5 HOH A 56 1056 8 HOH HOH . 
G 5 HOH A 57 1057 40 HOH HOH . 
G 5 HOH A 58 1058 39 HOH HOH . 
G 5 HOH A 59 1059 144 HOH HOH . 
G 5 HOH A 60 1060 1 HOH HOH . 
G 5 HOH A 61 1061 57 HOH HOH . 
G 5 HOH A 62 1062 156 HOH HOH . 
G 5 HOH A 63 1063 50 HOH HOH . 
G 5 HOH A 64 1064 5 HOH HOH . 
G 5 HOH A 65 1065 100 HOH HOH . 
G 5 HOH A 66 1066 70 HOH HOH . 
G 5 HOH A 67 1067 17 HOH HOH . 
G 5 HOH A 68 1068 141 HOH HOH . 
G 5 HOH A 69 1069 92 HOH HOH . 
G 5 HOH A 70 1070 91 HOH HOH . 
G 5 HOH A 71 1071 52 HOH HOH . 
G 5 HOH A 72 1072 30 HOH HOH . 
G 5 HOH A 73 1073 174 HOH HOH . 
G 5 HOH A 74 1074 72 HOH HOH . 
G 5 HOH A 75 1075 78 HOH HOH . 
G 5 HOH A 76 1076 98 HOH HOH . 
G 5 HOH A 77 1077 26 HOH HOH . 
G 5 HOH A 78 1078 105 HOH HOH . 
G 5 HOH A 79 1079 93 HOH HOH . 
G 5 HOH A 80 1080 56 HOH HOH . 
G 5 HOH A 81 1081 171 HOH HOH . 
G 5 HOH A 82 1082 68 HOH HOH . 
G 5 HOH A 83 1083 9 HOH HOH . 
G 5 HOH A 84 1084 157 HOH HOH . 
G 5 HOH A 85 1085 42 HOH HOH . 
G 5 HOH A 86 1086 67 HOH HOH . 
G 5 HOH A 87 1087 159 HOH HOH . 
G 5 HOH A 88 1088 120 HOH HOH . 
G 5 HOH A 89 1089 27 HOH HOH . 
G 5 HOH A 90 1090 71 HOH HOH . 
G 5 HOH A 91 1091 165 HOH HOH . 
G 5 HOH A 92 1092 18 HOH HOH . 
G 5 HOH A 93 1093 184 HOH HOH . 
G 5 HOH A 94 1094 160 HOH HOH . 
G 5 HOH A 95 1095 139 HOH HOH . 
G 5 HOH A 96 1096 196 HOH HOH . 
G 5 HOH A 97 1097 55 HOH HOH . 
G 5 HOH A 98 1098 126 HOH HOH . 
G 5 HOH A 99 1099 65 HOH HOH . 
G 5 HOH A 100 1100 14 HOH HOH . 
G 5 HOH A 101 1101 32 HOH HOH . 
G 5 HOH A 102 1102 107 HOH HOH . 
G 5 HOH A 103 1103 59 HOH HOH . 
G 5 HOH A 104 1104 28 HOH HOH . 
G 5 HOH A 105 1105 135 HOH HOH . 
G 5 HOH A 106 1106 116 HOH HOH . 
G 5 HOH A 107 1107 36 HOH HOH . 
G 5 HOH A 108 1108 2 HOH HOH . 
G 5 HOH A 109 1109 94 HOH HOH . 
G 5 HOH A 110 1110 112 HOH HOH . 
G 5 HOH A 111 1111 19 HOH HOH . 
G 5 HOH A 112 1112 95 HOH HOH . 
G 5 HOH A 113 1113 31 HOH HOH . 
G 5 HOH A 114 1114 123 HOH HOH . 
G 5 HOH A 115 1115 151 HOH HOH . 
G 5 HOH A 116 1116 150 HOH HOH . 
G 5 HOH A 117 1117 178 HOH HOH . 
G 5 HOH A 118 1118 179 HOH HOH . 
G 5 HOH A 119 1119 75 HOH HOH . 
G 5 HOH A 120 1120 121 HOH HOH . 
G 5 HOH A 121 1121 88 HOH HOH . 
G 5 HOH A 122 1122 33 HOH HOH . 
G 5 HOH A 123 1123 186 HOH HOH . 
G 5 HOH A 124 1124 45 HOH HOH . 
G 5 HOH A 125 1125 73 HOH HOH . 
G 5 HOH A 126 1126 147 HOH HOH . 
G 5 HOH A 127 1127 103 HOH HOH . 
G 5 HOH A 128 1128 11 HOH HOH . 
G 5 HOH A 129 1129 142 HOH HOH . 
G 5 HOH A 130 1130 131 HOH HOH . 
G 5 HOH A 131 1131 148 HOH HOH . 
G 5 HOH A 132 1132 163 HOH HOH . 
G 5 HOH A 133 1133 146 HOH HOH . 
G 5 HOH A 134 1134 167 HOH HOH . 
G 5 HOH A 135 1135 23 HOH HOH . 
G 5 HOH A 136 1136 158 HOH HOH . 
G 5 HOH A 137 1137 137 HOH HOH . 
G 5 HOH A 138 1138 191 HOH HOH . 
G 5 HOH A 139 1139 140 HOH HOH . 
G 5 HOH A 140 1140 185 HOH HOH . 
G 5 HOH A 141 1141 152 HOH HOH . 
G 5 HOH A 142 1142 182 HOH HOH . 
G 5 HOH A 143 1143 69 HOH HOH . 
G 5 HOH A 144 1144 122 HOH HOH . 
G 5 HOH A 145 1145 87 HOH HOH . 
G 5 HOH A 146 1146 54 HOH HOH . 
G 5 HOH A 147 1147 37 HOH HOH . 
G 5 HOH A 148 1148 101 HOH HOH . 
G 5 HOH A 149 1149 170 HOH HOH . 
G 5 HOH A 150 1150 153 HOH HOH . 
G 5 HOH A 151 1151 66 HOH HOH . 
G 5 HOH A 152 1152 155 HOH HOH . 
G 5 HOH A 153 1153 58 HOH HOH . 
G 5 HOH A 154 1154 161 HOH HOH . 
G 5 HOH A 155 1155 115 HOH HOH . 
G 5 HOH A 156 1156 118 HOH HOH . 
G 5 HOH A 157 1157 113 HOH HOH . 
G 5 HOH A 158 1158 172 HOH HOH . 
G 5 HOH A 159 1159 136 HOH HOH . 
G 5 HOH A 160 1160 119 HOH HOH . 
G 5 HOH A 161 1161 190 HOH HOH . 
G 5 HOH A 162 1162 108 HOH HOH . 
G 5 HOH A 163 1163 175 HOH HOH . 
G 5 HOH A 164 1164 102 HOH HOH . 
G 5 HOH A 165 1165 128 HOH HOH . 
G 5 HOH A 166 1166 97 HOH HOH . 
G 5 HOH A 167 1167 82 HOH HOH . 
G 5 HOH A 168 1168 49 HOH HOH . 
G 5 HOH A 169 1169 188 HOH HOH . 
G 5 HOH A 170 1170 90 HOH HOH . 
H 5 HOH B 1 101 76 HOH HOH . 
H 5 HOH B 2 102 111 HOH HOH . 
H 5 HOH B 3 103 127 HOH HOH . 
H 5 HOH B 4 104 138 HOH HOH . 
H 5 HOH B 5 105 10 HOH HOH . 
H 5 HOH B 6 106 187 HOH HOH . 
H 5 HOH B 7 107 129 HOH HOH . 
H 5 HOH B 8 108 84 HOH HOH . 
H 5 HOH B 9 109 53 HOH HOH . 
H 5 HOH B 10 110 63 HOH HOH . 
H 5 HOH B 11 111 62 HOH HOH . 
H 5 HOH B 12 112 134 HOH HOH . 
H 5 HOH B 13 113 189 HOH HOH . 
H 5 HOH B 14 114 192 HOH HOH . 
H 5 HOH B 15 115 194 HOH HOH . 
H 5 HOH B 16 116 195 HOH HOH . 
H 5 HOH B 17 117 130 HOH HOH . 
H 5 HOH B 18 118 24 HOH HOH . 
H 5 HOH B 19 119 106 HOH HOH . 
H 5 HOH B 20 120 77 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 . . . D 4 -15.58 -18.495 -21.579 1 32.55 ? C1 EDO 902 A 1 
HETATM 2 O O1 EDO . . . D 4 -14.86 -19.324 -20.679 1 28.93 ? O1 EDO 902 A 1 
HETATM 3 C C2 EDO . . . D 4 -15.558 -17.062 -21.075 1 32.86 ? C2 EDO 902 A 1 
HETATM 4 O O2 EDO . . . D 4 -15.256 -16.158 -22.159 1 36.38 ? O2 EDO 902 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           4 
#