data_5EBU # _model_server_result.job_id Upwy_vdziDDQ84PnI8jz2g _model_server_result.datetime_utc '2024-12-01 09:05:23' _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 5ebu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":401}' # _entry.id 5EBU # _exptl.entry_id 5EBU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.52 _cell.angle_gamma 90 _cell.entry_id 5EBU _cell.length_a 107.346 _cell.length_b 119.184 _cell.length_c 119.56 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EBU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L,M,N,O,P,Y,Z,AA,BA 1 1 E,F,G,H,Q,R,S,T,U,V,W,X,CA,DA,EA,FA 2 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 ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N N ? 3 T N N ? 3 V N N ? 3 X N N # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC ACID' _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 C O PYR doub 318 n n C OXT PYR sing 319 n n C CA PYR sing 320 n n OXT HXT PYR sing 321 n n CA O3 PYR doub 322 n n CA CB PYR sing 323 n n CB HB1 PYR sing 324 n n CB HB2 PYR sing 325 n n CB HB3 PYR sing 326 n n # _atom_sites.entry_id 5EBU _atom_sites.fract_transf_matrix[1][1] 0.009316 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00294 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00839 _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] 0.008771 _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 I 2 FMN A 1 400 400 FMN FMN . J 3 PYR A 1 401 401 PYR PYR . K 2 FMN B 1 400 400 FMN FMN . L 3 PYR B 1 401 401 PYR PYR . M 2 FMN C 1 400 400 FMN FMN . N 3 PYR C 1 401 401 PYR PYR . O 2 FMN D 1 400 400 FMN FMN . P 3 PYR D 1 401 401 PYR PYR . Q 2 FMN E 1 400 400 FMN FMN . R 3 PYR E 1 401 401 PYR PYR . S 2 FMN F 1 400 400 FMN FMN . T 3 PYR F 1 401 401 PYR PYR . U 2 FMN G 1 400 400 FMN FMN . V 3 PYR G 1 401 401 PYR PYR . W 2 FMN H 1 400 400 FMN FMN . X 3 PYR H 1 401 401 PYR PYR . Y 4 HOH A 1 501 97 HOH HOH . Y 4 HOH A 2 502 210 HOH HOH . Y 4 HOH A 3 503 209 HOH HOH . Y 4 HOH A 4 504 119 HOH HOH . Y 4 HOH A 5 505 136 HOH HOH . Y 4 HOH A 6 506 137 HOH HOH . Y 4 HOH A 7 507 160 HOH HOH . Y 4 HOH A 8 508 208 HOH HOH . Y 4 HOH A 9 509 75 HOH HOH . Y 4 HOH A 10 510 59 HOH HOH . Y 4 HOH A 11 511 2 HOH HOH . Y 4 HOH A 12 512 254 HOH HOH . Y 4 HOH A 13 513 6 HOH HOH . Y 4 HOH A 14 514 130 HOH HOH . Y 4 HOH A 15 515 162 HOH HOH . Y 4 HOH A 16 516 53 HOH HOH . Y 4 HOH A 17 517 64 HOH HOH . Y 4 HOH A 18 518 165 HOH HOH . Y 4 HOH A 19 519 116 HOH HOH . Y 4 HOH A 20 520 133 HOH HOH . Y 4 HOH A 21 521 128 HOH HOH . Y 4 HOH A 22 522 73 HOH HOH . Y 4 HOH A 23 523 134 HOH HOH . Y 4 HOH A 24 524 161 HOH HOH . Y 4 HOH A 25 525 135 HOH HOH . Y 4 HOH A 26 526 118 HOH HOH . Y 4 HOH A 27 527 23 HOH HOH . Y 4 HOH A 28 528 110 HOH HOH . Y 4 HOH A 29 529 164 HOH HOH . Y 4 HOH A 30 530 163 HOH HOH . Y 4 HOH A 31 531 92 HOH HOH . Y 4 HOH A 32 532 19 HOH HOH . Z 4 HOH B 1 501 244 HOH HOH . Z 4 HOH B 2 502 166 HOH HOH . Z 4 HOH B 3 503 201 HOH HOH . Z 4 HOH B 4 504 213 HOH HOH . Z 4 HOH B 5 505 63 HOH HOH . Z 4 HOH B 6 506 243 HOH HOH . Z 4 HOH B 7 507 91 HOH HOH . Z 4 HOH B 8 508 25 HOH HOH . Z 4 HOH B 9 509 170 HOH HOH . Z 4 HOH B 10 510 132 HOH HOH . Z 4 HOH B 11 511 195 HOH HOH . Z 4 HOH B 12 512 131 HOH HOH . Z 4 HOH B 13 513 5 HOH HOH . Z 4 HOH B 14 514 198 HOH HOH . Z 4 HOH B 15 515 196 HOH HOH . Z 4 HOH B 16 516 129 HOH HOH . Z 4 HOH B 17 517 10 HOH HOH . Z 4 HOH B 18 518 86 HOH HOH . Z 4 HOH B 19 519 22 HOH HOH . Z 4 HOH B 20 520 138 HOH HOH . Z 4 HOH B 21 521 16 HOH HOH . Z 4 HOH B 22 522 95 HOH HOH . Z 4 HOH B 23 523 197 HOH HOH . Z 4 HOH B 24 524 24 HOH HOH . Z 4 HOH B 25 525 58 HOH HOH . Z 4 HOH B 26 526 242 HOH HOH . Z 4 HOH B 27 527 270 HOH HOH . Z 4 HOH B 28 528 88 HOH HOH . Z 4 HOH B 29 529 167 HOH HOH . Z 4 HOH B 30 530 29 HOH HOH . Z 4 HOH B 31 531 8 HOH HOH . Z 4 HOH B 32 532 35 HOH HOH . Z 4 HOH B 33 533 37 HOH HOH . Z 4 HOH B 34 534 30 HOH HOH . Z 4 HOH B 35 535 120 HOH HOH . Z 4 HOH B 36 536 206 HOH HOH . Z 4 HOH B 37 537 199 HOH HOH . Z 4 HOH B 38 538 27 HOH HOH . Z 4 HOH B 39 539 200 HOH HOH . Z 4 HOH B 40 540 67 HOH HOH . Z 4 HOH B 41 541 44 HOH HOH . Z 4 HOH B 42 542 57 HOH HOH . Z 4 HOH B 43 543 245 HOH HOH . Z 4 HOH B 44 544 74 HOH HOH . Z 4 HOH B 45 545 207 HOH HOH . Z 4 HOH B 46 546 169 HOH HOH . Z 4 HOH B 47 547 49 HOH HOH . AA 4 HOH C 1 501 111 HOH HOH . AA 4 HOH C 2 502 78 HOH HOH . AA 4 HOH C 3 503 127 HOH HOH . AA 4 HOH C 4 504 11 HOH HOH . AA 4 HOH C 5 505 141 HOH HOH . AA 4 HOH C 6 506 77 HOH HOH . AA 4 HOH C 7 507 253 HOH HOH . AA 4 HOH C 8 508 214 HOH HOH . AA 4 HOH C 9 509 212 HOH HOH . AA 4 HOH C 10 510 113 HOH HOH . AA 4 HOH C 11 511 248 HOH HOH . AA 4 HOH C 12 512 140 HOH HOH . AA 4 HOH C 13 513 139 HOH HOH . AA 4 HOH C 14 514 211 HOH HOH . AA 4 HOH C 15 515 104 HOH HOH . AA 4 HOH C 16 516 103 HOH HOH . AA 4 HOH C 17 517 252 HOH HOH . AA 4 HOH C 18 518 109 HOH HOH . AA 4 HOH C 19 519 80 HOH HOH . AA 4 HOH C 20 520 100 HOH HOH . AA 4 HOH C 21 521 217 HOH HOH . AA 4 HOH C 22 522 247 HOH HOH . AA 4 HOH C 23 523 215 HOH HOH . AA 4 HOH C 24 524 251 HOH HOH . AA 4 HOH C 25 525 246 HOH HOH . BA 4 HOH D 1 501 168 HOH HOH . BA 4 HOH D 2 502 121 HOH HOH . BA 4 HOH D 3 503 15 HOH HOH . BA 4 HOH D 4 504 79 HOH HOH . BA 4 HOH D 5 505 144 HOH HOH . BA 4 HOH D 6 506 204 HOH HOH . BA 4 HOH D 7 507 250 HOH HOH . BA 4 HOH D 8 508 269 HOH HOH . BA 4 HOH D 9 509 268 HOH HOH . BA 4 HOH D 10 510 17 HOH HOH . BA 4 HOH D 11 511 101 HOH HOH . BA 4 HOH D 12 512 142 HOH HOH . BA 4 HOH D 13 513 216 HOH HOH . BA 4 HOH D 14 514 143 HOH HOH . BA 4 HOH D 15 515 249 HOH HOH . BA 4 HOH D 16 516 203 HOH HOH . BA 4 HOH D 17 517 205 HOH HOH . BA 4 HOH D 18 518 96 HOH HOH . BA 4 HOH D 19 519 52 HOH HOH . BA 4 HOH D 20 520 202 HOH HOH . BA 4 HOH D 21 521 56 HOH HOH . BA 4 HOH D 22 522 42 HOH HOH . BA 4 HOH D 23 523 12 HOH HOH . CA 4 HOH E 1 501 145 HOH HOH . CA 4 HOH E 2 502 177 HOH HOH . CA 4 HOH E 3 503 218 HOH HOH . CA 4 HOH E 4 504 178 HOH HOH . CA 4 HOH E 5 505 238 HOH HOH . CA 4 HOH E 6 506 34 HOH HOH . CA 4 HOH E 7 507 175 HOH HOH . CA 4 HOH E 8 508 47 HOH HOH . CA 4 HOH E 9 509 7 HOH HOH . CA 4 HOH E 10 510 172 HOH HOH . CA 4 HOH E 11 511 146 HOH HOH . CA 4 HOH E 12 512 48 HOH HOH . CA 4 HOH E 13 513 72 HOH HOH . CA 4 HOH E 14 514 237 HOH HOH . CA 4 HOH E 15 515 115 HOH HOH . CA 4 HOH E 16 516 176 HOH HOH . CA 4 HOH E 17 517 147 HOH HOH . CA 4 HOH E 18 518 14 HOH HOH . CA 4 HOH E 19 519 117 HOH HOH . CA 4 HOH E 20 520 236 HOH HOH . CA 4 HOH E 21 521 171 HOH HOH . CA 4 HOH E 22 522 126 HOH HOH . CA 4 HOH E 23 523 185 HOH HOH . CA 4 HOH E 24 524 99 HOH HOH . CA 4 HOH E 25 525 232 HOH HOH . CA 4 HOH E 26 526 233 HOH HOH . CA 4 HOH E 27 527 61 HOH HOH . CA 4 HOH E 28 528 240 HOH HOH . CA 4 HOH E 29 529 239 HOH HOH . CA 4 HOH E 30 530 184 HOH HOH . CA 4 HOH E 31 531 40 HOH HOH . CA 4 HOH E 32 532 148 HOH HOH . CA 4 HOH E 33 533 43 HOH HOH . CA 4 HOH E 34 534 21 HOH HOH . CA 4 HOH E 35 535 60 HOH HOH . CA 4 HOH E 36 536 50 HOH HOH . DA 4 HOH F 1 501 85 HOH HOH . DA 4 HOH F 2 502 180 HOH HOH . DA 4 HOH F 3 503 84 HOH HOH . DA 4 HOH F 4 504 149 HOH HOH . DA 4 HOH F 5 505 70 HOH HOH . DA 4 HOH F 6 506 221 HOH HOH . DA 4 HOH F 7 507 255 HOH HOH . DA 4 HOH F 8 508 83 HOH HOH . DA 4 HOH F 9 509 9 HOH HOH . DA 4 HOH F 10 510 256 HOH HOH . DA 4 HOH F 11 511 174 HOH HOH . DA 4 HOH F 12 512 46 HOH HOH . DA 4 HOH F 13 513 173 HOH HOH . DA 4 HOH F 14 514 220 HOH HOH . DA 4 HOH F 15 515 272 HOH HOH . DA 4 HOH F 16 516 66 HOH HOH . DA 4 HOH F 17 517 3 HOH HOH . DA 4 HOH F 18 518 151 HOH HOH . DA 4 HOH F 19 519 183 HOH HOH . DA 4 HOH F 20 520 264 HOH HOH . DA 4 HOH F 21 521 68 HOH HOH . DA 4 HOH F 22 522 271 HOH HOH . DA 4 HOH F 23 523 181 HOH HOH . DA 4 HOH F 24 524 273 HOH HOH . DA 4 HOH F 25 525 108 HOH HOH . DA 4 HOH F 26 526 18 HOH HOH . DA 4 HOH F 27 527 81 HOH HOH . DA 4 HOH F 28 528 45 HOH HOH . DA 4 HOH F 29 529 179 HOH HOH . DA 4 HOH F 30 530 153 HOH HOH . DA 4 HOH F 31 531 98 HOH HOH . DA 4 HOH F 32 532 219 HOH HOH . DA 4 HOH F 33 533 125 HOH HOH . DA 4 HOH F 34 534 152 HOH HOH . DA 4 HOH F 35 535 87 HOH HOH . DA 4 HOH F 36 536 182 HOH HOH . EA 4 HOH G 1 501 186 HOH HOH . EA 4 HOH G 2 502 193 HOH HOH . EA 4 HOH G 3 503 265 HOH HOH . EA 4 HOH G 4 504 54 HOH HOH . EA 4 HOH G 5 505 231 HOH HOH . EA 4 HOH G 6 506 114 HOH HOH . EA 4 HOH G 7 507 124 HOH HOH . EA 4 HOH G 8 508 227 HOH HOH . EA 4 HOH G 9 509 190 HOH HOH . EA 4 HOH G 10 510 191 HOH HOH . EA 4 HOH G 11 511 228 HOH HOH . EA 4 HOH G 12 512 102 HOH HOH . EA 4 HOH G 13 513 65 HOH HOH . EA 4 HOH G 14 514 123 HOH HOH . EA 4 HOH G 15 515 154 HOH HOH . EA 4 HOH G 16 516 258 HOH HOH . EA 4 HOH G 17 517 82 HOH HOH . EA 4 HOH G 18 518 189 HOH HOH . EA 4 HOH G 19 519 187 HOH HOH . EA 4 HOH G 20 520 13 HOH HOH . EA 4 HOH G 21 521 263 HOH HOH . EA 4 HOH G 22 522 39 HOH HOH . EA 4 HOH G 23 523 266 HOH HOH . EA 4 HOH G 24 524 89 HOH HOH . EA 4 HOH G 25 525 155 HOH HOH . EA 4 HOH G 26 526 226 HOH HOH . EA 4 HOH G 27 527 105 HOH HOH . EA 4 HOH G 28 528 93 HOH HOH . EA 4 HOH G 29 529 222 HOH HOH . EA 4 HOH G 30 530 234 HOH HOH . EA 4 HOH G 31 531 51 HOH HOH . EA 4 HOH G 32 532 224 HOH HOH . EA 4 HOH G 33 533 188 HOH HOH . EA 4 HOH G 34 534 262 HOH HOH . EA 4 HOH G 35 535 106 HOH HOH . EA 4 HOH G 36 536 122 HOH HOH . EA 4 HOH G 37 537 223 HOH HOH . EA 4 HOH G 38 538 267 HOH HOH . EA 4 HOH G 39 539 107 HOH HOH . FA 4 HOH H 1 501 150 HOH HOH . FA 4 HOH H 2 502 194 HOH HOH . FA 4 HOH H 3 503 36 HOH HOH . FA 4 HOH H 4 504 94 HOH HOH . FA 4 HOH H 5 505 230 HOH HOH . FA 4 HOH H 6 506 33 HOH HOH . FA 4 HOH H 7 507 90 HOH HOH . FA 4 HOH H 8 508 38 HOH HOH . FA 4 HOH H 9 509 26 HOH HOH . FA 4 HOH H 10 510 31 HOH HOH . FA 4 HOH H 11 511 71 HOH HOH . FA 4 HOH H 12 512 62 HOH HOH . FA 4 HOH H 13 513 192 HOH HOH . FA 4 HOH H 14 514 32 HOH HOH . FA 4 HOH H 15 515 112 HOH HOH . FA 4 HOH H 16 516 261 HOH HOH . FA 4 HOH H 17 517 156 HOH HOH . FA 4 HOH H 18 518 69 HOH HOH . FA 4 HOH H 19 519 28 HOH HOH . FA 4 HOH H 20 520 157 HOH HOH . FA 4 HOH H 21 521 55 HOH HOH . FA 4 HOH H 22 522 41 HOH HOH . FA 4 HOH H 23 523 259 HOH HOH . FA 4 HOH H 24 524 229 HOH HOH . FA 4 HOH H 25 525 159 HOH HOH . FA 4 HOH H 26 526 158 HOH HOH . FA 4 HOH H 27 527 1 HOH HOH . FA 4 HOH H 28 528 4 HOH HOH . FA 4 HOH H 29 529 260 HOH HOH . FA 4 HOH H 30 530 76 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 C PYR . . . X 3 20.841 113.44 89.281 1 59.18 ? C PYR 401 H 1 HETATM 2 O O PYR . . . X 3 21.967 112.905 89.282 1 57.36 ? O PYR 401 H 1 HETATM 3 O OXT PYR . . . X 3 19.956 113.004 90.052 1 55.82 ? OXT PYR 401 H 1 HETATM 4 C CA PYR . . . X 3 20.569 114.593 88.387 1 61.93 ? CA PYR 401 H 1 HETATM 5 O O3 PYR . . . X 3 21.221 115.615 88.533 1 62.19 ? O3 PYR 401 H 1 HETATM 6 C CB PYR . . . X 3 19.505 114.543 87.312 1 60.05 ? CB PYR 401 H 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #