data_5WYD # _model_server_result.job_id IymDoBgfukhgD0qQKr-6xg _model_server_result.datetime_utc '2024-11-14 20:36:36' _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":"N","auth_seq_id":302}' # _entry.id 5WYD # _exptl.entry_id 5WYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 100.116 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PENTANEDIAL _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 L N N ? 2 N N N # _chem_comp.formula 'C5 H8 O2' _chem_comp.formula_weight 100.116 _chem_comp.id PTD _chem_comp.mon_nstd_flag . _chem_comp.name PENTANEDIAL _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 PTD sing 330 n n C1 O1 PTD doub 331 n n C1 HC1 PTD sing 332 n n C2 C3 PTD sing 333 n n C2 HC21 PTD sing 334 n n C2 HC22 PTD sing 335 n n C3 C4 PTD sing 336 n n C3 HC31 PTD sing 337 n n C3 HC32 PTD sing 338 n n C4 C5 PTD sing 339 n n C4 HC41 PTD sing 340 n n C4 HC42 PTD sing 341 n n C5 O5 PTD doub 342 n n C5 HC5 PTD sing 343 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 PTD . . . N 2 -68.209 66.801 -22.025 1 35.49 ? C1 PTD 302 E 1 HETATM 2 C C2 PTD . . . N 2 -69.204 67.464 -21.056 1 28.01 ? C2 PTD 302 E 1 HETATM 3 C C3 PTD . . . N 2 -70.669 67.48 -21.521 1 10.78 ? C3 PTD 302 E 1 HETATM 4 C C4 PTD . . . N 2 -70.959 66.347 -22.461 1 22.45 ? C4 PTD 302 E 1 HETATM 5 C C5 PTD . . . N 2 -71.238 66.709 -23.929 1 34.77 ? C5 PTD 302 E 1 HETATM 6 O O1 PTD . . . N 2 -68.039 65.622 -22.026 1 21.91 ? O1 PTD 302 E 1 HETATM 7 O O5 PTD . . . N 2 -70.897 66.003 -24.859 1 32.99 ? O5 PTD 302 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 70 _model_server_stats.query_time_ms 614 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 7 #