data_5WYD # _model_server_result.job_id OpUu1tWLblzfV3v6uq3bwg _model_server_result.datetime_utc '2024-11-14 20:23:05' _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 5wyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":303}' # _entry.id 5WYD # _exptl.entry_id 5WYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5WYD _cell.length_a 83.309 _cell.length_b 83.309 _cell.length_c 207.547 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,G,H,I,J,K,L,S,T,U,V 1 1 F,O,P,Q,R,X 1 2 E,M,N,W 1 3 # 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' 1_665 x+1,y+1,z 1 0 0 0 1 0 0 0 1 41.6545 72.14771 0 3 'crystal symmetry operation' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 83.309 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id K _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C2 MPD sing 248 n n C1 H11 MPD sing 249 n n C1 H12 MPD sing 250 n n C1 H13 MPD sing 251 n n C2 O2 MPD sing 252 n n C2 CM MPD sing 253 n n C2 C3 MPD sing 254 n n O2 HO2 MPD sing 255 n n CM HM1 MPD sing 256 n n CM HM2 MPD sing 257 n n CM HM3 MPD sing 258 n n C3 C4 MPD sing 259 n n C3 H31 MPD sing 260 n n C3 H32 MPD sing 261 n n C4 O4 MPD sing 262 n n C4 C5 MPD sing 263 n n C4 H4 MPD sing 264 n n O4 HO4 MPD sing 265 n n C5 H51 MPD sing 266 n n C5 H52 MPD sing 267 n n C5 H53 MPD sing 268 n n # _atom_sites.entry_id 5WYD _atom_sites.fract_transf_matrix[1][1] 0.012004 _atom_sites.fract_transf_matrix[1][2] 0.00693 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01386 _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] 0.004818 _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 G 2 PTD A 1 301 1 PTD LIG . H 3 IPA B 1 301 4 IPA IPA . I 3 IPA C 1 301 1 IPA IPA . J 3 IPA C 1 302 2 IPA IPA . K 4 MPD C 1 303 1 MPD MPD . L 2 PTD D 1 301 3 PTD LIG . M 3 IPA E 1 301 3 IPA IPA . N 2 PTD E 1 302 2 PTD LIG . O 3 IPA F 1 301 5 IPA IPA . P 3 IPA F 1 302 6 IPA IPA . Q 3 IPA F 1 303 7 IPA IPA . R 5 MRD F 1 304 2 MRD MPD . S 6 HOH A 1 401 11 HOH HOH . S 6 HOH A 2 402 97 HOH HOH . S 6 HOH A 3 403 138 HOH HOH . S 6 HOH A 4 404 131 HOH HOH . S 6 HOH A 5 405 51 HOH HOH . S 6 HOH A 6 406 130 HOH HOH . S 6 HOH A 7 407 27 HOH HOH . S 6 HOH A 8 408 35 HOH HOH . S 6 HOH A 9 409 55 HOH HOH . S 6 HOH A 10 410 104 HOH HOH . S 6 HOH A 11 411 56 HOH HOH . S 6 HOH A 12 412 141 HOH HOH . S 6 HOH A 13 413 21 HOH HOH . S 6 HOH A 14 414 37 HOH HOH . S 6 HOH A 15 415 114 HOH HOH . S 6 HOH A 16 416 17 HOH HOH . S 6 HOH A 17 417 135 HOH HOH . S 6 HOH A 18 418 31 HOH HOH . S 6 HOH A 19 419 2 HOH HOH . S 6 HOH A 20 420 64 HOH HOH . S 6 HOH A 21 421 41 HOH HOH . S 6 HOH A 22 422 103 HOH HOH . S 6 HOH A 23 423 129 HOH HOH . S 6 HOH A 24 424 140 HOH HOH . S 6 HOH A 25 425 157 HOH HOH . S 6 HOH A 26 426 48 HOH HOH . S 6 HOH A 27 427 148 HOH HOH . S 6 HOH A 28 428 113 HOH HOH . S 6 HOH A 29 429 170 HOH HOH . S 6 HOH A 30 430 199 HOH HOH . T 6 HOH B 1 401 33 HOH HOH . T 6 HOH B 2 402 91 HOH HOH . T 6 HOH B 3 403 167 HOH HOH . T 6 HOH B 4 404 14 HOH HOH . T 6 HOH B 5 405 111 HOH HOH . T 6 HOH B 6 406 71 HOH HOH . T 6 HOH B 7 407 30 HOH HOH . T 6 HOH B 8 408 54 HOH HOH . T 6 HOH B 9 409 8 HOH HOH . T 6 HOH B 10 410 26 HOH HOH . T 6 HOH B 11 411 136 HOH HOH . T 6 HOH B 12 412 145 HOH HOH . T 6 HOH B 13 413 85 HOH HOH . T 6 HOH B 14 414 29 HOH HOH . T 6 HOH B 15 415 46 HOH HOH . T 6 HOH B 16 416 137 HOH HOH . T 6 HOH B 17 417 160 HOH HOH . T 6 HOH B 18 418 123 HOH HOH . T 6 HOH B 19 419 156 HOH HOH . T 6 HOH B 20 420 166 HOH HOH . T 6 HOH B 21 421 165 HOH HOH . T 6 HOH B 22 422 92 HOH HOH . T 6 HOH B 23 423 109 HOH HOH . T 6 HOH B 24 424 112 HOH HOH . T 6 HOH B 25 425 70 HOH HOH . T 6 HOH B 26 426 65 HOH HOH . T 6 HOH B 27 427 78 HOH HOH . T 6 HOH B 28 428 168 HOH HOH . T 6 HOH B 29 429 185 HOH HOH . T 6 HOH B 30 430 164 HOH HOH . T 6 HOH B 31 431 186 HOH HOH . T 6 HOH B 32 432 187 HOH HOH . U 6 HOH C 1 401 44 HOH HOH . U 6 HOH C 2 402 105 HOH HOH . U 6 HOH C 3 403 142 HOH HOH . U 6 HOH C 4 404 20 HOH HOH . U 6 HOH C 5 405 150 HOH HOH . U 6 HOH C 6 406 67 HOH HOH . U 6 HOH C 7 407 101 HOH HOH . U 6 HOH C 8 408 28 HOH HOH . U 6 HOH C 9 409 139 HOH HOH . U 6 HOH C 10 410 38 HOH HOH . U 6 HOH C 11 411 32 HOH HOH . U 6 HOH C 12 412 12 HOH HOH . U 6 HOH C 13 413 171 HOH HOH . U 6 HOH C 14 414 102 HOH HOH . U 6 HOH C 15 415 61 HOH HOH . U 6 HOH C 16 416 106 HOH HOH . U 6 HOH C 17 417 80 HOH HOH . U 6 HOH C 18 418 43 HOH HOH . U 6 HOH C 19 419 95 HOH HOH . U 6 HOH C 20 420 100 HOH HOH . U 6 HOH C 21 421 45 HOH HOH . U 6 HOH C 22 422 174 HOH HOH . U 6 HOH C 23 423 66 HOH HOH . U 6 HOH C 24 424 189 HOH HOH . U 6 HOH C 25 425 122 HOH HOH . U 6 HOH C 26 426 188 HOH HOH . U 6 HOH C 27 427 58 HOH HOH . U 6 HOH C 28 428 203 HOH HOH . U 6 HOH C 29 429 155 HOH HOH . U 6 HOH C 30 430 180 HOH HOH . U 6 HOH C 31 431 159 HOH HOH . U 6 HOH C 32 432 198 HOH HOH . U 6 HOH C 33 433 208 HOH HOH . U 6 HOH C 34 434 163 HOH HOH . U 6 HOH C 35 435 207 HOH HOH . U 6 HOH C 36 436 201 HOH HOH . V 6 HOH D 1 401 158 HOH HOH . V 6 HOH D 2 402 125 HOH HOH . V 6 HOH D 3 403 19 HOH HOH . V 6 HOH D 4 404 5 HOH HOH . V 6 HOH D 5 405 4 HOH HOH . V 6 HOH D 6 406 69 HOH HOH . V 6 HOH D 7 407 40 HOH HOH . V 6 HOH D 8 408 34 HOH HOH . V 6 HOH D 9 409 108 HOH HOH . V 6 HOH D 10 410 68 HOH HOH . V 6 HOH D 11 411 18 HOH HOH . V 6 HOH D 12 412 182 HOH HOH . V 6 HOH D 13 413 16 HOH HOH . V 6 HOH D 14 414 88 HOH HOH . V 6 HOH D 15 415 13 HOH HOH . V 6 HOH D 16 416 119 HOH HOH . V 6 HOH D 17 417 195 HOH HOH . V 6 HOH D 18 418 47 HOH HOH . V 6 HOH D 19 419 124 HOH HOH . V 6 HOH D 20 420 84 HOH HOH . V 6 HOH D 21 421 90 HOH HOH . V 6 HOH D 22 422 25 HOH HOH . V 6 HOH D 23 423 82 HOH HOH . V 6 HOH D 24 424 93 HOH HOH . V 6 HOH D 25 425 128 HOH HOH . V 6 HOH D 26 426 190 HOH HOH . V 6 HOH D 27 427 146 HOH HOH . V 6 HOH D 28 428 154 HOH HOH . V 6 HOH D 29 429 204 HOH HOH . W 6 HOH E 1 401 117 HOH HOH . W 6 HOH E 2 402 107 HOH HOH . W 6 HOH E 3 403 73 HOH HOH . W 6 HOH E 4 404 6 HOH HOH . W 6 HOH E 5 405 126 HOH HOH . W 6 HOH E 6 406 89 HOH HOH . W 6 HOH E 7 407 110 HOH HOH . W 6 HOH E 8 408 52 HOH HOH . W 6 HOH E 9 409 115 HOH HOH . W 6 HOH E 10 410 99 HOH HOH . W 6 HOH E 11 411 57 HOH HOH . W 6 HOH E 12 412 42 HOH HOH . W 6 HOH E 13 413 59 HOH HOH . W 6 HOH E 14 414 3 HOH HOH . W 6 HOH E 15 415 133 HOH HOH . W 6 HOH E 16 416 94 HOH HOH . W 6 HOH E 17 417 60 HOH HOH . W 6 HOH E 18 418 62 HOH HOH . W 6 HOH E 19 419 39 HOH HOH . W 6 HOH E 20 420 151 HOH HOH . W 6 HOH E 21 421 72 HOH HOH . W 6 HOH E 22 422 172 HOH HOH . W 6 HOH E 23 423 177 HOH HOH . W 6 HOH E 24 424 147 HOH HOH . W 6 HOH E 25 425 183 HOH HOH . W 6 HOH E 26 426 194 HOH HOH . W 6 HOH E 27 427 179 HOH HOH . W 6 HOH E 28 428 205 HOH HOH . W 6 HOH E 29 429 202 HOH HOH . W 6 HOH E 30 430 173 HOH HOH . W 6 HOH E 31 431 178 HOH HOH . W 6 HOH E 32 432 181 HOH HOH . W 6 HOH E 33 433 197 HOH HOH . X 6 HOH F 1 401 50 HOH HOH . X 6 HOH F 2 402 23 HOH HOH . X 6 HOH F 3 403 149 HOH HOH . X 6 HOH F 4 404 10 HOH HOH . X 6 HOH F 5 405 134 HOH HOH . X 6 HOH F 6 406 49 HOH HOH . X 6 HOH F 7 407 24 HOH HOH . X 6 HOH F 8 408 200 HOH HOH . X 6 HOH F 9 409 161 HOH HOH . X 6 HOH F 10 410 98 HOH HOH . X 6 HOH F 11 411 53 HOH HOH . X 6 HOH F 12 412 127 HOH HOH . X 6 HOH F 13 413 120 HOH HOH . X 6 HOH F 14 414 74 HOH HOH . X 6 HOH F 15 415 96 HOH HOH . X 6 HOH F 16 416 176 HOH HOH . X 6 HOH F 17 417 121 HOH HOH . X 6 HOH F 18 418 152 HOH HOH . X 6 HOH F 19 419 83 HOH HOH . X 6 HOH F 20 420 193 HOH HOH . X 6 HOH F 21 421 206 HOH HOH . X 6 HOH F 22 422 118 HOH HOH . X 6 HOH F 23 423 9 HOH HOH . X 6 HOH F 24 424 144 HOH HOH . X 6 HOH F 25 425 162 HOH HOH . X 6 HOH F 26 426 175 HOH HOH . X 6 HOH F 27 427 196 HOH HOH . X 6 HOH F 28 428 192 HOH HOH . X 6 HOH F 29 429 153 HOH HOH . X 6 HOH F 30 430 116 HOH HOH . X 6 HOH F 31 431 169 HOH HOH . X 6 HOH F 32 432 191 HOH HOH . X 6 HOH F 33 433 184 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 MPD . . . K 4 -46.437 38.022 -46.84 1 54 ? C1 MPD 303 C 1 HETATM 2 C C2 MPD . . . K 4 -45.479 38.805 -45.924 1 42.82 ? C2 MPD 303 C 1 HETATM 3 O O2 MPD . . . K 4 -44.41 39.479 -46.704 1 43.08 ? O2 MPD 303 C 1 HETATM 4 C CM MPD . . . K 4 -46.29 39.827 -45.188 1 53.09 ? CM MPD 303 C 1 HETATM 5 C C3 MPD . . . K 4 -44.766 37.715 -45.157 1 29.07 ? C3 MPD 303 C 1 HETATM 6 C C4 MPD . . . K 4 -43.852 36.976 -46.155 1 26.18 ? C4 MPD 303 C 1 HETATM 7 O O4 MPD . . . K 4 -43.059 37.939 -46.806 1 39.36 ? O4 MPD 303 C 1 HETATM 8 C C5 MPD . . . K 4 -42.966 35.9 -45.509 1 30.61 ? C5 MPD 303 C 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 447 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 8 #