data_5VND # _model_server_result.job_id qwZf2GxdKKVQHI3nF8Uzuw _model_server_result.datetime_utc '2024-11-14 18:21:01' _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 5vnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":809}' # _entry.id 5VND # _exptl.entry_id 5VND _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 15 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.59 _cell.angle_gamma 90 _cell.entry_id 5VND _cell.length_a 208.494 _cell.length_b 58.925 _cell.length_c 65.935 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VND _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N,X 1 1 B,O,P,Q,R,S,T,U,V,W,Y 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y 3 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 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W 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 A SG CYS 107 A CYS 563 1_555 C C27 9ES . A 9ES 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? covale ? covale2 B SG CYS 107 B CYS 563 1_555 O C27 9ES . B 9ES 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? # _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 165 n n C1 C2 EDO sing 166 n n C1 H11 EDO sing 167 n n C1 H12 EDO sing 168 n n O1 HO1 EDO sing 169 n n C2 O2 EDO sing 170 n n C2 H21 EDO sing 171 n n C2 H22 EDO sing 172 n n O2 HO2 EDO sing 173 n n # _atom_sites.entry_id 5VND _atom_sites.fract_transf_matrix[1][1] 0.004796 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00152 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016971 _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] 0.01591 _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 9ES A 1 801 2 9ES 527 . D 3 SO4 A 1 802 1 SO4 SO4 . E 3 SO4 A 1 803 3 SO4 SO4 . F 4 EDO A 1 804 1 EDO EDO . G 4 EDO A 1 805 2 EDO EDO . H 4 EDO A 1 806 4 EDO EDO . I 4 EDO A 1 807 5 EDO EDO . J 4 EDO A 1 808 6 EDO EDO . K 4 EDO A 1 809 7 EDO EDO . L 4 EDO A 1 810 8 EDO EDO . M 4 EDO A 1 811 11 EDO EDO . N 4 EDO A 1 812 15 EDO EDO . O 2 9ES B 1 801 1 9ES 527 . P 3 SO4 B 1 802 2 SO4 SO4 . Q 3 SO4 B 1 803 5 SO4 SO4 . R 4 EDO B 1 804 3 EDO EDO . S 4 EDO B 1 805 9 EDO EDO . T 4 EDO B 1 806 10 EDO EDO . U 4 EDO B 1 807 12 EDO EDO . V 4 EDO B 1 808 13 EDO EDO . W 4 EDO B 1 809 14 EDO EDO . X 5 HOH A 1 901 175 HOH HOH . X 5 HOH A 2 902 78 HOH HOH . X 5 HOH A 3 903 129 HOH HOH . X 5 HOH A 4 904 235 HOH HOH . X 5 HOH A 5 905 23 HOH HOH . X 5 HOH A 6 906 223 HOH HOH . X 5 HOH A 7 907 216 HOH HOH . X 5 HOH A 8 908 105 HOH HOH . X 5 HOH A 9 909 213 HOH HOH . X 5 HOH A 10 910 26 HOH HOH . X 5 HOH A 11 911 25 HOH HOH . X 5 HOH A 12 912 15 HOH HOH . X 5 HOH A 13 913 256 HOH HOH . X 5 HOH A 14 914 212 HOH HOH . X 5 HOH A 15 915 14 HOH HOH . X 5 HOH A 16 916 120 HOH HOH . X 5 HOH A 17 917 225 HOH HOH . X 5 HOH A 18 918 16 HOH HOH . X 5 HOH A 19 919 232 HOH HOH . X 5 HOH A 20 920 96 HOH HOH . X 5 HOH A 21 921 76 HOH HOH . X 5 HOH A 22 922 145 HOH HOH . X 5 HOH A 23 923 2 HOH HOH . X 5 HOH A 24 924 87 HOH HOH . X 5 HOH A 25 925 193 HOH HOH . X 5 HOH A 26 926 89 HOH HOH . X 5 HOH A 27 927 156 HOH HOH . X 5 HOH A 28 928 22 HOH HOH . X 5 HOH A 29 929 248 HOH HOH . X 5 HOH A 30 930 254 HOH HOH . X 5 HOH A 31 931 84 HOH HOH . X 5 HOH A 32 932 45 HOH HOH . X 5 HOH A 33 933 21 HOH HOH . X 5 HOH A 34 934 62 HOH HOH . X 5 HOH A 35 935 4 HOH HOH . X 5 HOH A 36 936 165 HOH HOH . X 5 HOH A 37 937 189 HOH HOH . X 5 HOH A 38 938 13 HOH HOH . X 5 HOH A 39 939 242 HOH HOH . X 5 HOH A 40 940 67 HOH HOH . X 5 HOH A 41 941 231 HOH HOH . X 5 HOH A 42 942 215 HOH HOH . X 5 HOH A 43 943 135 HOH HOH . X 5 HOH A 44 944 203 HOH HOH . X 5 HOH A 45 945 66 HOH HOH . X 5 HOH A 46 946 79 HOH HOH . X 5 HOH A 47 947 214 HOH HOH . X 5 HOH A 48 948 101 HOH HOH . X 5 HOH A 49 949 32 HOH HOH . X 5 HOH A 50 950 177 HOH HOH . X 5 HOH A 51 951 179 HOH HOH . X 5 HOH A 52 952 219 HOH HOH . X 5 HOH A 53 953 88 HOH HOH . X 5 HOH A 54 954 115 HOH HOH . X 5 HOH A 55 955 245 HOH HOH . X 5 HOH A 56 956 8 HOH HOH . X 5 HOH A 57 957 108 HOH HOH . X 5 HOH A 58 958 142 HOH HOH . X 5 HOH A 59 959 54 HOH HOH . X 5 HOH A 60 960 18 HOH HOH . X 5 HOH A 61 961 222 HOH HOH . X 5 HOH A 62 962 162 HOH HOH . X 5 HOH A 63 963 121 HOH HOH . X 5 HOH A 64 964 141 HOH HOH . X 5 HOH A 65 965 116 HOH HOH . X 5 HOH A 66 966 257 HOH HOH . X 5 HOH A 67 967 102 HOH HOH . X 5 HOH A 68 968 60 HOH HOH . X 5 HOH A 69 969 224 HOH HOH . X 5 HOH A 70 970 153 HOH HOH . X 5 HOH A 71 971 71 HOH HOH . X 5 HOH A 72 972 48 HOH HOH . X 5 HOH A 73 973 176 HOH HOH . X 5 HOH A 74 974 107 HOH HOH . X 5 HOH A 75 975 20 HOH HOH . X 5 HOH A 76 976 17 HOH HOH . X 5 HOH A 77 977 55 HOH HOH . X 5 HOH A 78 978 92 HOH HOH . X 5 HOH A 79 979 93 HOH HOH . X 5 HOH A 80 980 72 HOH HOH . X 5 HOH A 81 981 173 HOH HOH . X 5 HOH A 82 982 63 HOH HOH . X 5 HOH A 83 983 163 HOH HOH . X 5 HOH A 84 984 188 HOH HOH . X 5 HOH A 85 985 56 HOH HOH . X 5 HOH A 86 986 51 HOH HOH . X 5 HOH A 87 987 33 HOH HOH . X 5 HOH A 88 988 154 HOH HOH . X 5 HOH A 89 989 139 HOH HOH . X 5 HOH A 90 990 253 HOH HOH . X 5 HOH A 91 991 147 HOH HOH . X 5 HOH A 92 992 61 HOH HOH . X 5 HOH A 93 993 98 HOH HOH . X 5 HOH A 94 994 137 HOH HOH . X 5 HOH A 95 995 83 HOH HOH . X 5 HOH A 96 996 157 HOH HOH . X 5 HOH A 97 997 237 HOH HOH . X 5 HOH A 98 998 150 HOH HOH . X 5 HOH A 99 999 64 HOH HOH . X 5 HOH A 100 1000 198 HOH HOH . X 5 HOH A 101 1001 230 HOH HOH . X 5 HOH A 102 1002 52 HOH HOH . X 5 HOH A 103 1003 255 HOH HOH . X 5 HOH A 104 1004 110 HOH HOH . X 5 HOH A 105 1005 152 HOH HOH . X 5 HOH A 106 1006 234 HOH HOH . X 5 HOH A 107 1007 228 HOH HOH . X 5 HOH A 108 1008 57 HOH HOH . X 5 HOH A 109 1009 240 HOH HOH . X 5 HOH A 110 1010 210 HOH HOH . X 5 HOH A 111 1011 250 HOH HOH . X 5 HOH A 112 1012 233 HOH HOH . X 5 HOH A 113 1013 11 HOH HOH . X 5 HOH A 114 1014 201 HOH HOH . X 5 HOH A 115 1015 50 HOH HOH . X 5 HOH A 116 1016 206 HOH HOH . X 5 HOH A 117 1017 187 HOH HOH . X 5 HOH A 118 1018 251 HOH HOH . X 5 HOH A 119 1019 204 HOH HOH . X 5 HOH A 120 1020 258 HOH HOH . X 5 HOH A 121 1021 199 HOH HOH . X 5 HOH A 122 1022 168 HOH HOH . X 5 HOH A 123 1023 252 HOH HOH . X 5 HOH A 124 1024 249 HOH HOH . Y 5 HOH B 1 901 195 HOH HOH . Y 5 HOH B 2 902 131 HOH HOH . Y 5 HOH B 3 903 184 HOH HOH . Y 5 HOH B 4 904 217 HOH HOH . Y 5 HOH B 5 905 172 HOH HOH . Y 5 HOH B 6 906 191 HOH HOH . Y 5 HOH B 7 907 6 HOH HOH . Y 5 HOH B 8 908 161 HOH HOH . Y 5 HOH B 9 909 7 HOH HOH . Y 5 HOH B 10 910 169 HOH HOH . Y 5 HOH B 11 911 3 HOH HOH . Y 5 HOH B 12 912 151 HOH HOH . Y 5 HOH B 13 913 82 HOH HOH . Y 5 HOH B 14 914 218 HOH HOH . Y 5 HOH B 15 915 133 HOH HOH . Y 5 HOH B 16 916 221 HOH HOH . Y 5 HOH B 17 917 69 HOH HOH . Y 5 HOH B 18 918 27 HOH HOH . Y 5 HOH B 19 919 130 HOH HOH . Y 5 HOH B 20 920 259 HOH HOH . Y 5 HOH B 21 921 106 HOH HOH . Y 5 HOH B 22 922 81 HOH HOH . Y 5 HOH B 23 923 158 HOH HOH . Y 5 HOH B 24 924 111 HOH HOH . Y 5 HOH B 25 925 86 HOH HOH . Y 5 HOH B 26 926 44 HOH HOH . Y 5 HOH B 27 927 136 HOH HOH . Y 5 HOH B 28 928 236 HOH HOH . Y 5 HOH B 29 929 125 HOH HOH . Y 5 HOH B 30 930 10 HOH HOH . Y 5 HOH B 31 931 166 HOH HOH . Y 5 HOH B 32 932 91 HOH HOH . Y 5 HOH B 33 933 47 HOH HOH . Y 5 HOH B 34 934 1 HOH HOH . Y 5 HOH B 35 935 220 HOH HOH . Y 5 HOH B 36 936 132 HOH HOH . Y 5 HOH B 37 937 134 HOH HOH . Y 5 HOH B 38 938 53 HOH HOH . Y 5 HOH B 39 939 207 HOH HOH . Y 5 HOH B 40 940 174 HOH HOH . Y 5 HOH B 41 941 118 HOH HOH . Y 5 HOH B 42 942 49 HOH HOH . Y 5 HOH B 43 943 167 HOH HOH . Y 5 HOH B 44 944 103 HOH HOH . Y 5 HOH B 45 945 9 HOH HOH . Y 5 HOH B 46 946 5 HOH HOH . Y 5 HOH B 47 947 149 HOH HOH . Y 5 HOH B 48 948 85 HOH HOH . Y 5 HOH B 49 949 119 HOH HOH . Y 5 HOH B 50 950 80 HOH HOH . Y 5 HOH B 51 951 138 HOH HOH . Y 5 HOH B 52 952 126 HOH HOH . Y 5 HOH B 53 953 94 HOH HOH . Y 5 HOH B 54 954 238 HOH HOH . Y 5 HOH B 55 955 59 HOH HOH . Y 5 HOH B 56 956 117 HOH HOH . Y 5 HOH B 57 957 36 HOH HOH . Y 5 HOH B 58 958 155 HOH HOH . Y 5 HOH B 59 959 227 HOH HOH . Y 5 HOH B 60 960 19 HOH HOH . Y 5 HOH B 61 961 112 HOH HOH . Y 5 HOH B 62 962 144 HOH HOH . Y 5 HOH B 63 963 140 HOH HOH . Y 5 HOH B 64 964 40 HOH HOH . Y 5 HOH B 65 965 190 HOH HOH . Y 5 HOH B 66 966 164 HOH HOH . Y 5 HOH B 67 967 95 HOH HOH . Y 5 HOH B 68 968 58 HOH HOH . Y 5 HOH B 69 969 192 HOH HOH . Y 5 HOH B 70 970 181 HOH HOH . Y 5 HOH B 71 971 41 HOH HOH . Y 5 HOH B 72 972 24 HOH HOH . Y 5 HOH B 73 973 65 HOH HOH . Y 5 HOH B 74 974 186 HOH HOH . Y 5 HOH B 75 975 73 HOH HOH . Y 5 HOH B 76 976 70 HOH HOH . Y 5 HOH B 77 977 241 HOH HOH . Y 5 HOH B 78 978 37 HOH HOH . Y 5 HOH B 79 979 104 HOH HOH . Y 5 HOH B 80 980 229 HOH HOH . Y 5 HOH B 81 981 39 HOH HOH . Y 5 HOH B 82 982 148 HOH HOH . Y 5 HOH B 83 983 178 HOH HOH . Y 5 HOH B 84 984 38 HOH HOH . Y 5 HOH B 85 985 34 HOH HOH . Y 5 HOH B 86 986 77 HOH HOH . Y 5 HOH B 87 987 246 HOH HOH . Y 5 HOH B 88 988 183 HOH HOH . Y 5 HOH B 89 989 35 HOH HOH . Y 5 HOH B 90 990 68 HOH HOH . Y 5 HOH B 91 991 124 HOH HOH . Y 5 HOH B 92 992 113 HOH HOH . Y 5 HOH B 93 993 159 HOH HOH . Y 5 HOH B 94 994 75 HOH HOH . Y 5 HOH B 95 995 160 HOH HOH . Y 5 HOH B 96 996 122 HOH HOH . Y 5 HOH B 97 997 127 HOH HOH . Y 5 HOH B 98 998 12 HOH HOH . Y 5 HOH B 99 999 30 HOH HOH . Y 5 HOH B 100 1000 180 HOH HOH . Y 5 HOH B 101 1001 29 HOH HOH . Y 5 HOH B 102 1002 143 HOH HOH . Y 5 HOH B 103 1003 99 HOH HOH . Y 5 HOH B 104 1004 200 HOH HOH . Y 5 HOH B 105 1005 46 HOH HOH . Y 5 HOH B 106 1006 247 HOH HOH . Y 5 HOH B 107 1007 90 HOH HOH . Y 5 HOH B 108 1008 97 HOH HOH . Y 5 HOH B 109 1009 123 HOH HOH . Y 5 HOH B 110 1010 211 HOH HOH . Y 5 HOH B 111 1011 226 HOH HOH . Y 5 HOH B 112 1012 185 HOH HOH . Y 5 HOH B 113 1013 244 HOH HOH . Y 5 HOH B 114 1014 182 HOH HOH . Y 5 HOH B 115 1015 209 HOH HOH . Y 5 HOH B 116 1016 109 HOH HOH . Y 5 HOH B 117 1017 243 HOH HOH . Y 5 HOH B 118 1018 170 HOH HOH . Y 5 HOH B 119 1019 202 HOH HOH . Y 5 HOH B 120 1020 197 HOH HOH . Y 5 HOH B 121 1021 239 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 . . . W 4 91.929 -26.668 -12.061 1 72.14 ? C1 EDO 809 B 1 HETATM 2 O O1 EDO . . . W 4 91.218 -27.831 -12.497 1 74.72 ? O1 EDO 809 B 1 HETATM 3 C C2 EDO . . . W 4 91.958 -26.72 -10.537 1 74.7 ? C2 EDO 809 B 1 HETATM 4 O O2 EDO . . . W 4 92.691 -25.616 -9.979 1 81.7 ? O2 EDO 809 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 4 #