data_5KD7 # _model_server_result.job_id aJGMiCx7VZUhkiyqa5hN1Q _model_server_result.datetime_utc '2025-01-10 20:00:25' _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 5kd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":102}' # _entry.id 5KD7 # _exptl.entry_id 5KD7 _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 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 93.52 _cell.angle_beta 87.14 _cell.angle_gamma 96.5 _cell.entry_id 5KD7 _cell.length_a 51.42 _cell.length_b 75.36 _cell.length_c 120.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KD7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,M,N,O,V,W,X 1 1 D,E,F,P,Y,Z,AA 2 1 G,H,I,Q,R,S,T,BA,CA,DA 3 1 J,K,L,U,EA,FA,GA 4 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 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 R N N ? 4 S N N ? 4 U 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 disulf ? disulf1 A SG CYS 100 A CYS 101 1_555 A SG CYS 163 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 202 A CYS 203 1_555 A SG CYS 258 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 D SG CYS 100 C CYS 101 1_555 D SG CYS 163 C CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 D SG CYS 202 C CYS 203 1_555 D SG CYS 258 C CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 E SG CYS 26 D CYS 25 1_555 E SG CYS 81 D CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 G SG CYS 100 F CYS 101 1_555 G SG CYS 163 F CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 G SG CYS 202 F CYS 203 1_555 G SG CYS 258 F CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf9 H SG CYS 26 G CYS 25 1_555 H SG CYS 81 G CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 J SG CYS 100 I CYS 101 1_555 J SG CYS 163 I CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 J SG CYS 202 I CYS 203 1_555 J SG CYS 258 I CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 K SG CYS 26 J CYS 25 1_555 K SG CYS 81 J CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _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 5KD7 _atom_sites.fract_transf_matrix[1][1] 0.019448 _atom_sites.fract_transf_matrix[1][2] 0.002215 _atom_sites.fract_transf_matrix[1][3] -0.000849 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013355 _atom_sites.fract_transf_matrix[2][3] 0.00075 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008355 _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 M 4 EDO A 1 301 4 EDO EDO . N 4 EDO B 1 101 5 EDO EDO . O 4 EDO B 1 102 9 EDO EDO . P 4 EDO D 1 101 6 EDO EDO . Q 5 GOL F 1 301 1 GOL GOL . R 4 EDO F 1 302 2 EDO EDO . S 4 EDO F 1 303 7 EDO EDO . T 5 GOL F 1 304 8 GOL GOL . U 4 EDO I 1 301 3 EDO EDO . V 6 HOH A 1 401 100 HOH HOH . V 6 HOH A 2 402 101 HOH HOH . V 6 HOH A 3 403 15 HOH HOH . V 6 HOH A 4 404 26 HOH HOH . V 6 HOH A 5 405 118 HOH HOH . V 6 HOH A 6 406 199 HOH HOH . V 6 HOH A 7 407 66 HOH HOH . V 6 HOH A 8 408 141 HOH HOH . V 6 HOH A 9 409 203 HOH HOH . V 6 HOH A 10 410 56 HOH HOH . V 6 HOH A 11 411 201 HOH HOH . V 6 HOH A 12 412 184 HOH HOH . V 6 HOH A 13 413 44 HOH HOH . V 6 HOH A 14 414 152 HOH HOH . V 6 HOH A 15 415 182 HOH HOH . V 6 HOH A 16 416 49 HOH HOH . V 6 HOH A 17 417 111 HOH HOH . V 6 HOH A 18 418 70 HOH HOH . V 6 HOH A 19 419 206 HOH HOH . V 6 HOH A 20 420 17 HOH HOH . V 6 HOH A 21 421 54 HOH HOH . V 6 HOH A 22 422 63 HOH HOH . V 6 HOH A 23 423 19 HOH HOH . V 6 HOH A 24 424 6 HOH HOH . V 6 HOH A 25 425 68 HOH HOH . V 6 HOH A 26 426 116 HOH HOH . V 6 HOH A 27 427 125 HOH HOH . V 6 HOH A 28 428 30 HOH HOH . V 6 HOH A 29 429 138 HOH HOH . V 6 HOH A 30 430 45 HOH HOH . V 6 HOH A 31 431 215 HOH HOH . V 6 HOH A 32 432 11 HOH HOH . V 6 HOH A 33 433 191 HOH HOH . V 6 HOH A 34 434 65 HOH HOH . V 6 HOH A 35 435 172 HOH HOH . V 6 HOH A 36 436 164 HOH HOH . V 6 HOH A 37 437 153 HOH HOH . V 6 HOH A 38 438 178 HOH HOH . V 6 HOH A 39 439 181 HOH HOH . V 6 HOH A 40 440 130 HOH HOH . V 6 HOH A 41 441 37 HOH HOH . V 6 HOH A 42 442 207 HOH HOH . V 6 HOH A 43 443 92 HOH HOH . V 6 HOH A 44 444 220 HOH HOH . V 6 HOH A 45 445 75 HOH HOH . V 6 HOH A 46 446 87 HOH HOH . V 6 HOH A 47 447 102 HOH HOH . W 6 HOH B 1 201 175 HOH HOH . W 6 HOH B 2 202 5 HOH HOH . W 6 HOH B 3 203 123 HOH HOH . W 6 HOH B 4 204 38 HOH HOH . W 6 HOH B 5 205 53 HOH HOH . W 6 HOH B 6 206 46 HOH HOH . W 6 HOH B 7 207 173 HOH HOH . W 6 HOH B 8 208 73 HOH HOH . W 6 HOH B 9 209 60 HOH HOH . W 6 HOH B 10 210 21 HOH HOH . W 6 HOH B 11 211 52 HOH HOH . W 6 HOH B 12 212 57 HOH HOH . W 6 HOH B 13 213 43 HOH HOH . W 6 HOH B 14 214 81 HOH HOH . W 6 HOH B 15 215 106 HOH HOH . W 6 HOH B 16 216 40 HOH HOH . W 6 HOH B 17 217 189 HOH HOH . W 6 HOH B 18 218 161 HOH HOH . W 6 HOH B 19 219 78 HOH HOH . W 6 HOH B 20 220 195 HOH HOH . W 6 HOH B 21 221 23 HOH HOH . W 6 HOH B 22 222 41 HOH HOH . W 6 HOH B 23 223 80 HOH HOH . W 6 HOH B 24 224 188 HOH HOH . W 6 HOH B 25 225 62 HOH HOH . W 6 HOH B 26 226 58 HOH HOH . W 6 HOH B 27 227 146 HOH HOH . W 6 HOH B 28 228 136 HOH HOH . X 6 HOH P 1 101 39 HOH HOH . X 6 HOH P 2 102 179 HOH HOH . Y 6 HOH C 1 301 166 HOH HOH . Y 6 HOH C 2 302 142 HOH HOH . Y 6 HOH C 3 303 148 HOH HOH . Y 6 HOH C 4 304 8 HOH HOH . Y 6 HOH C 5 305 2 HOH HOH . Y 6 HOH C 6 306 155 HOH HOH . Y 6 HOH C 7 307 29 HOH HOH . Y 6 HOH C 8 308 82 HOH HOH . Y 6 HOH C 9 309 83 HOH HOH . Y 6 HOH C 10 310 149 HOH HOH . Y 6 HOH C 11 311 77 HOH HOH . Y 6 HOH C 12 312 202 HOH HOH . Y 6 HOH C 13 313 158 HOH HOH . Y 6 HOH C 14 314 114 HOH HOH . Y 6 HOH C 15 315 10 HOH HOH . Y 6 HOH C 16 316 18 HOH HOH . Y 6 HOH C 17 317 132 HOH HOH . Y 6 HOH C 18 318 176 HOH HOH . Y 6 HOH C 19 319 120 HOH HOH . Y 6 HOH C 20 320 187 HOH HOH . Y 6 HOH C 21 321 1 HOH HOH . Y 6 HOH C 22 322 147 HOH HOH . Y 6 HOH C 23 323 90 HOH HOH . Y 6 HOH C 24 324 4 HOH HOH . Y 6 HOH C 25 325 196 HOH HOH . Y 6 HOH C 26 326 193 HOH HOH . Y 6 HOH C 27 327 154 HOH HOH . Y 6 HOH C 28 328 105 HOH HOH . Y 6 HOH C 29 329 137 HOH HOH . Y 6 HOH C 30 330 74 HOH HOH . Y 6 HOH C 31 331 79 HOH HOH . Y 6 HOH C 32 332 210 HOH HOH . Y 6 HOH C 33 333 150 HOH HOH . Y 6 HOH C 34 334 212 HOH HOH . Y 6 HOH C 35 335 119 HOH HOH . Y 6 HOH C 36 336 69 HOH HOH . Y 6 HOH C 37 337 98 HOH HOH . Y 6 HOH C 38 338 171 HOH HOH . Y 6 HOH C 39 339 185 HOH HOH . Y 6 HOH C 40 340 135 HOH HOH . Y 6 HOH C 41 341 84 HOH HOH . Y 6 HOH C 42 342 205 HOH HOH . Z 6 HOH D 1 201 88 HOH HOH . Z 6 HOH D 2 202 192 HOH HOH . Z 6 HOH D 3 203 33 HOH HOH . Z 6 HOH D 4 204 127 HOH HOH . Z 6 HOH D 5 205 85 HOH HOH . AA 6 HOH E 1 101 14 HOH HOH . AA 6 HOH E 2 102 218 HOH HOH . BA 6 HOH F 1 401 170 HOH HOH . BA 6 HOH F 2 402 204 HOH HOH . BA 6 HOH F 3 403 13 HOH HOH . BA 6 HOH F 4 404 20 HOH HOH . BA 6 HOH F 5 405 115 HOH HOH . BA 6 HOH F 6 406 194 HOH HOH . BA 6 HOH F 7 407 162 HOH HOH . BA 6 HOH F 8 408 131 HOH HOH . BA 6 HOH F 9 409 71 HOH HOH . BA 6 HOH F 10 410 36 HOH HOH . BA 6 HOH F 11 411 126 HOH HOH . BA 6 HOH F 12 412 42 HOH HOH . BA 6 HOH F 13 413 27 HOH HOH . BA 6 HOH F 14 414 156 HOH HOH . BA 6 HOH F 15 415 177 HOH HOH . BA 6 HOH F 16 416 32 HOH HOH . BA 6 HOH F 17 417 24 HOH HOH . BA 6 HOH F 18 418 145 HOH HOH . BA 6 HOH F 19 419 200 HOH HOH . BA 6 HOH F 20 420 86 HOH HOH . BA 6 HOH F 21 421 48 HOH HOH . BA 6 HOH F 22 422 107 HOH HOH . BA 6 HOH F 23 423 89 HOH HOH . BA 6 HOH F 24 424 197 HOH HOH . BA 6 HOH F 25 425 12 HOH HOH . BA 6 HOH F 26 426 34 HOH HOH . BA 6 HOH F 27 427 31 HOH HOH . BA 6 HOH F 28 428 7 HOH HOH . BA 6 HOH F 29 429 140 HOH HOH . BA 6 HOH F 30 430 47 HOH HOH . BA 6 HOH F 31 431 186 HOH HOH . BA 6 HOH F 32 432 59 HOH HOH . BA 6 HOH F 33 433 28 HOH HOH . BA 6 HOH F 34 434 112 HOH HOH . BA 6 HOH F 35 435 72 HOH HOH . BA 6 HOH F 36 436 96 HOH HOH . BA 6 HOH F 37 437 169 HOH HOH . BA 6 HOH F 38 438 35 HOH HOH . BA 6 HOH F 39 439 139 HOH HOH . BA 6 HOH F 40 440 143 HOH HOH . BA 6 HOH F 41 441 167 HOH HOH . BA 6 HOH F 42 442 208 HOH HOH . BA 6 HOH F 43 443 51 HOH HOH . BA 6 HOH F 44 444 113 HOH HOH . BA 6 HOH F 45 445 198 HOH HOH . CA 6 HOH G 1 101 217 HOH HOH . CA 6 HOH G 2 102 16 HOH HOH . CA 6 HOH G 3 103 163 HOH HOH . CA 6 HOH G 4 104 128 HOH HOH . CA 6 HOH G 5 105 97 HOH HOH . CA 6 HOH G 6 106 151 HOH HOH . CA 6 HOH G 7 107 95 HOH HOH . CA 6 HOH G 8 108 121 HOH HOH . CA 6 HOH G 9 109 64 HOH HOH . CA 6 HOH G 10 110 9 HOH HOH . CA 6 HOH G 11 111 99 HOH HOH . CA 6 HOH G 12 112 3 HOH HOH . CA 6 HOH G 13 113 159 HOH HOH . CA 6 HOH G 14 114 174 HOH HOH . CA 6 HOH G 15 115 103 HOH HOH . CA 6 HOH G 16 116 165 HOH HOH . CA 6 HOH G 17 117 214 HOH HOH . CA 6 HOH G 18 118 67 HOH HOH . CA 6 HOH G 19 119 109 HOH HOH . CA 6 HOH G 20 120 91 HOH HOH . CA 6 HOH G 21 121 160 HOH HOH . CA 6 HOH G 22 122 76 HOH HOH . CA 6 HOH G 23 123 108 HOH HOH . CA 6 HOH G 24 124 157 HOH HOH . CA 6 HOH G 25 125 110 HOH HOH . CA 6 HOH G 26 126 134 HOH HOH . CA 6 HOH G 27 127 124 HOH HOH . CA 6 HOH G 28 128 50 HOH HOH . CA 6 HOH G 29 129 216 HOH HOH . CA 6 HOH G 30 130 219 HOH HOH . DA 6 HOH H 1 101 183 HOH HOH . EA 6 HOH I 1 401 213 HOH HOH . EA 6 HOH I 2 402 211 HOH HOH . EA 6 HOH I 3 403 22 HOH HOH . EA 6 HOH I 4 404 104 HOH HOH . EA 6 HOH I 5 405 94 HOH HOH . EA 6 HOH I 6 406 93 HOH HOH . EA 6 HOH I 7 407 55 HOH HOH . EA 6 HOH I 8 408 209 HOH HOH . EA 6 HOH I 9 409 122 HOH HOH . EA 6 HOH I 10 410 133 HOH HOH . FA 6 HOH J 1 101 180 HOH HOH . FA 6 HOH J 2 102 129 HOH HOH . FA 6 HOH J 3 103 61 HOH HOH . FA 6 HOH J 4 104 25 HOH HOH . FA 6 HOH J 5 105 190 HOH HOH . GA 6 HOH K 1 101 117 HOH HOH . GA 6 HOH K 2 102 168 HOH HOH . GA 6 HOH K 3 103 144 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 . . . O 4 -14.597 50.039 35.857 1 36.26 ? C1 EDO 102 B 1 HETATM 2 O O1 EDO . . . O 4 -16.013 50.232 36.006 1 33.64 ? O1 EDO 102 B 1 HETATM 3 C C2 EDO . . . O 4 -14.187 49.89 34.388 1 29.58 ? C2 EDO 102 B 1 HETATM 4 O O2 EDO . . . O 4 -14.603 51.027 33.602 1 25.94 ? O2 EDO 102 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 4 #