data_8VKD # _model_server_result.job_id O4KiGj673A8BkOmuRBBUVA _model_server_result.datetime_utc '2024-11-27 21:50:02' _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 8vkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":207}' # _entry.id 8VKD # _exptl.entry_id 8VKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 8VKD _cell.length_a 58.359 _cell.length_b 68.036 _cell.length_c 68.312 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # 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,O 1 1 B,K,L,M,N,P 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 D N N ? 3 I 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 ND1 HIS 55 AAA HIS 55 1_555 F O8 4NC . AAA 4NC 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale2 A CE1 HIS 55 AAA HIS 55 1_555 F C2 4NC . AAA 4NC 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.067 ? covale ? covale3 A CE1 HIS 55 AAA HIS 55 1_555 F C6 4NC . AAA 4NC 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.632 ? covale ? covale4 A NE2 HIS 55 AAA HIS 55 1_555 F C1 4NC . AAA 4NC 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale5 A NE2 HIS 55 AAA HIS 55 1_555 F C6 4NC . AAA 4NC 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale6 B ND1 HIS 55 BBB HIS 55 1_555 L C1 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.285 ? covale ? covale7 B ND1 HIS 55 BBB HIS 55 1_555 L O8 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale8 B CE1 HIS 55 BBB HIS 55 1_555 L C2 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale9 B CE1 HIS 55 BBB HIS 55 1_555 L C6 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.212 ? covale ? covale10 B NE2 HIS 55 BBB HIS 55 1_555 L C1 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.553 ? covale ? covale11 B NE2 HIS 55 BBB HIS 55 1_555 L C6 4NC . BBB 4NC 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.496 ? metalc ? metalc1 A NE2 HIS 89 AAA HIS 89 1_555 C FE HEM . AAA HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 C FE HEM . AAA HEM 201 1_555 O O HOH . AAA HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc3 B NE2 HIS 89 BBB HIS 89 1_555 K FE HEM . BBB HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 K FE HEM . BBB HEM 201 1_555 P O HOH . BBB HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 154 n n C1 C2 GOL sing 155 n n C1 H11 GOL sing 156 n n C1 H12 GOL sing 157 n n O1 HO1 GOL sing 158 n n C2 O2 GOL sing 159 n n C2 C3 GOL sing 160 n n C2 H2 GOL sing 161 n n O2 HO2 GOL sing 162 n n C3 O3 GOL sing 163 n n C3 H31 GOL sing 164 n n C3 H32 GOL sing 165 n n O3 HO3 GOL sing 166 n n # _atom_sites.entry_id 8VKD _atom_sites.fract_transf_matrix[1][1] 0.017135 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014698 _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] 0.014639 _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 HEM AAA 1 201 139 HEM HEM . D 3 GOL AAA 1 202 140 GOL GOL . E 4 PEG AAA 1 203 141 PEG PEG . F 5 4NC AAA 1 204 142 4NC 4NC . G 6 DMS AAA 1 205 143 DMS DMS . H 4 PEG AAA 1 206 144 PEG PEG . I 3 GOL AAA 1 207 146 GOL GOL . J 7 SO4 AAA 1 208 3 SO4 SO4 . K 2 HEM BBB 1 201 139 HEM HEM . L 5 4NC BBB 1 202 140 4NC 4NC . M 7 SO4 BBB 1 203 1 SO4 SO4 . N 7 SO4 BBB 1 204 2 SO4 SO4 . O 8 HOH AAA 1 301 12 HOH HOH . O 8 HOH AAA 2 302 42 HOH HOH . O 8 HOH AAA 3 303 95 HOH HOH . O 8 HOH AAA 4 304 98 HOH HOH . O 8 HOH AAA 5 305 210 HOH HOH . O 8 HOH AAA 6 306 159 HOH HOH . O 8 HOH AAA 7 307 72 HOH HOH . O 8 HOH AAA 8 308 75 HOH HOH . O 8 HOH AAA 9 309 211 HOH HOH . O 8 HOH AAA 10 310 109 HOH HOH . O 8 HOH AAA 11 311 204 HOH HOH . O 8 HOH AAA 12 312 47 HOH HOH . O 8 HOH AAA 13 313 163 HOH HOH . O 8 HOH AAA 14 314 76 HOH HOH . O 8 HOH AAA 15 315 223 HOH HOH . O 8 HOH AAA 16 316 36 HOH HOH . O 8 HOH AAA 17 317 200 HOH HOH . O 8 HOH AAA 18 318 92 HOH HOH . O 8 HOH AAA 19 319 82 HOH HOH . O 8 HOH AAA 20 320 114 HOH HOH . O 8 HOH AAA 21 321 91 HOH HOH . O 8 HOH AAA 22 322 29 HOH HOH . O 8 HOH AAA 23 323 15 HOH HOH . O 8 HOH AAA 24 324 40 HOH HOH . O 8 HOH AAA 25 325 89 HOH HOH . O 8 HOH AAA 26 326 102 HOH HOH . O 8 HOH AAA 27 327 79 HOH HOH . O 8 HOH AAA 28 328 209 HOH HOH . O 8 HOH AAA 29 329 85 HOH HOH . O 8 HOH AAA 30 330 58 HOH HOH . O 8 HOH AAA 31 331 94 HOH HOH . O 8 HOH AAA 32 332 24 HOH HOH . O 8 HOH AAA 33 333 201 HOH HOH . O 8 HOH AAA 34 334 203 HOH HOH . O 8 HOH AAA 35 335 84 HOH HOH . O 8 HOH AAA 36 336 74 HOH HOH . O 8 HOH AAA 37 337 14 HOH HOH . O 8 HOH AAA 38 338 67 HOH HOH . O 8 HOH AAA 39 339 6 HOH HOH . O 8 HOH AAA 40 340 7 HOH HOH . O 8 HOH AAA 41 341 13 HOH HOH . O 8 HOH AAA 42 342 146 HOH HOH . O 8 HOH AAA 43 343 65 HOH HOH . O 8 HOH AAA 44 344 108 HOH HOH . O 8 HOH AAA 45 345 50 HOH HOH . O 8 HOH AAA 46 346 11 HOH HOH . O 8 HOH AAA 47 347 131 HOH HOH . O 8 HOH AAA 48 348 22 HOH HOH . O 8 HOH AAA 49 349 48 HOH HOH . O 8 HOH AAA 50 350 63 HOH HOH . O 8 HOH AAA 51 351 81 HOH HOH . O 8 HOH AAA 52 352 34 HOH HOH . O 8 HOH AAA 53 353 66 HOH HOH . O 8 HOH AAA 54 354 104 HOH HOH . O 8 HOH AAA 55 355 52 HOH HOH . O 8 HOH AAA 56 356 161 HOH HOH . O 8 HOH AAA 57 357 55 HOH HOH . O 8 HOH AAA 58 358 26 HOH HOH . O 8 HOH AAA 59 359 57 HOH HOH . O 8 HOH AAA 60 360 41 HOH HOH . O 8 HOH AAA 61 361 212 HOH HOH . O 8 HOH AAA 62 362 68 HOH HOH . O 8 HOH AAA 63 363 31 HOH HOH . O 8 HOH AAA 64 364 150 HOH HOH . O 8 HOH AAA 65 365 33 HOH HOH . O 8 HOH AAA 66 366 103 HOH HOH . O 8 HOH AAA 67 367 38 HOH HOH . O 8 HOH AAA 68 368 208 HOH HOH . O 8 HOH AAA 69 369 71 HOH HOH . O 8 HOH AAA 70 370 59 HOH HOH . O 8 HOH AAA 71 371 147 HOH HOH . O 8 HOH AAA 72 372 120 HOH HOH . O 8 HOH AAA 73 373 158 HOH HOH . O 8 HOH AAA 74 374 125 HOH HOH . O 8 HOH AAA 75 375 206 HOH HOH . O 8 HOH AAA 76 376 160 HOH HOH . O 8 HOH AAA 77 377 133 HOH HOH . O 8 HOH AAA 78 378 148 HOH HOH . O 8 HOH AAA 79 379 45 HOH HOH . O 8 HOH AAA 80 380 78 HOH HOH . O 8 HOH AAA 81 381 205 HOH HOH . O 8 HOH AAA 82 382 144 HOH HOH . O 8 HOH AAA 83 383 100 HOH HOH . O 8 HOH AAA 84 384 44 HOH HOH . O 8 HOH AAA 85 385 162 HOH HOH . O 8 HOH AAA 86 386 1 HOH HOH . O 8 HOH AAA 87 387 145 HOH HOH . O 8 HOH AAA 88 388 142 HOH HOH . O 8 HOH AAA 89 389 207 HOH HOH . O 8 HOH AAA 90 390 112 HOH HOH . O 8 HOH AAA 91 391 137 HOH HOH . O 8 HOH AAA 92 392 214 HOH HOH . O 8 HOH AAA 93 393 119 HOH HOH . O 8 HOH AAA 94 394 127 HOH HOH . O 8 HOH AAA 95 395 105 HOH HOH . O 8 HOH AAA 96 396 140 HOH HOH . O 8 HOH AAA 97 397 199 HOH HOH . O 8 HOH AAA 98 398 96 HOH HOH . O 8 HOH AAA 99 399 141 HOH HOH . O 8 HOH AAA 100 400 124 HOH HOH . O 8 HOH AAA 101 401 101 HOH HOH . O 8 HOH AAA 102 402 62 HOH HOH . O 8 HOH AAA 103 403 116 HOH HOH . O 8 HOH AAA 104 404 115 HOH HOH . O 8 HOH AAA 105 405 61 HOH HOH . P 8 HOH BBB 1 301 123 HOH HOH . P 8 HOH BBB 2 302 32 HOH HOH . P 8 HOH BBB 3 303 178 HOH HOH . P 8 HOH BBB 4 304 53 HOH HOH . P 8 HOH BBB 5 305 179 HOH HOH . P 8 HOH BBB 6 306 171 HOH HOH . P 8 HOH BBB 7 307 165 HOH HOH . P 8 HOH BBB 8 308 164 HOH HOH . P 8 HOH BBB 9 309 220 HOH HOH . P 8 HOH BBB 10 310 181 HOH HOH . P 8 HOH BBB 11 311 25 HOH HOH . P 8 HOH BBB 12 312 222 HOH HOH . P 8 HOH BBB 13 313 157 HOH HOH . P 8 HOH BBB 14 314 17 HOH HOH . P 8 HOH BBB 15 315 30 HOH HOH . P 8 HOH BBB 16 316 192 HOH HOH . P 8 HOH BBB 17 317 166 HOH HOH . P 8 HOH BBB 18 318 156 HOH HOH . P 8 HOH BBB 19 319 90 HOH HOH . P 8 HOH BBB 20 320 87 HOH HOH . P 8 HOH BBB 21 321 27 HOH HOH . P 8 HOH BBB 22 322 153 HOH HOH . P 8 HOH BBB 23 323 190 HOH HOH . P 8 HOH BBB 24 324 175 HOH HOH . P 8 HOH BBB 25 325 173 HOH HOH . P 8 HOH BBB 26 326 198 HOH HOH . P 8 HOH BBB 27 327 185 HOH HOH . P 8 HOH BBB 28 328 51 HOH HOH . P 8 HOH BBB 29 329 4 HOH HOH . P 8 HOH BBB 30 330 152 HOH HOH . P 8 HOH BBB 31 331 182 HOH HOH . P 8 HOH BBB 32 332 218 HOH HOH . P 8 HOH BBB 33 333 187 HOH HOH . P 8 HOH BBB 34 334 18 HOH HOH . P 8 HOH BBB 35 335 189 HOH HOH . P 8 HOH BBB 36 336 9 HOH HOH . P 8 HOH BBB 37 337 177 HOH HOH . P 8 HOH BBB 38 338 19 HOH HOH . P 8 HOH BBB 39 339 169 HOH HOH . P 8 HOH BBB 40 340 5 HOH HOH . P 8 HOH BBB 41 341 8 HOH HOH . P 8 HOH BBB 42 342 49 HOH HOH . P 8 HOH BBB 43 343 60 HOH HOH . P 8 HOH BBB 44 344 186 HOH HOH . P 8 HOH BBB 45 345 154 HOH HOH . P 8 HOH BBB 46 346 170 HOH HOH . P 8 HOH BBB 47 347 73 HOH HOH . P 8 HOH BBB 48 348 70 HOH HOH . P 8 HOH BBB 49 349 216 HOH HOH . P 8 HOH BBB 50 350 217 HOH HOH . P 8 HOH BBB 51 351 113 HOH HOH . P 8 HOH BBB 52 352 151 HOH HOH . P 8 HOH BBB 53 353 176 HOH HOH . P 8 HOH BBB 54 354 132 HOH HOH . P 8 HOH BBB 55 355 219 HOH HOH . P 8 HOH BBB 56 356 10 HOH HOH . P 8 HOH BBB 57 357 196 HOH HOH . P 8 HOH BBB 58 358 193 HOH HOH . P 8 HOH BBB 59 359 16 HOH HOH . P 8 HOH BBB 60 360 184 HOH HOH . P 8 HOH BBB 61 361 21 HOH HOH . P 8 HOH BBB 62 362 20 HOH HOH . P 8 HOH BBB 63 363 215 HOH HOH . P 8 HOH BBB 64 364 135 HOH HOH . P 8 HOH BBB 65 365 110 HOH HOH . P 8 HOH BBB 66 366 191 HOH HOH . P 8 HOH BBB 67 367 188 HOH HOH . P 8 HOH BBB 68 368 86 HOH HOH . P 8 HOH BBB 69 369 221 HOH HOH . P 8 HOH BBB 70 370 3 HOH HOH . P 8 HOH BBB 71 371 168 HOH HOH . P 8 HOH BBB 72 372 77 HOH HOH . P 8 HOH BBB 73 373 35 HOH HOH . P 8 HOH BBB 74 374 83 HOH HOH . P 8 HOH BBB 75 375 64 HOH HOH . P 8 HOH BBB 76 376 155 HOH HOH . P 8 HOH BBB 77 377 97 HOH HOH . P 8 HOH BBB 78 378 80 HOH HOH . P 8 HOH BBB 79 379 183 HOH HOH . P 8 HOH BBB 80 380 172 HOH HOH . P 8 HOH BBB 81 381 195 HOH HOH . P 8 HOH BBB 82 382 88 HOH HOH . P 8 HOH BBB 83 383 128 HOH HOH . P 8 HOH BBB 84 384 194 HOH HOH . P 8 HOH BBB 85 385 99 HOH HOH . P 8 HOH BBB 86 386 107 HOH HOH . P 8 HOH BBB 87 387 121 HOH HOH . P 8 HOH BBB 88 388 118 HOH HOH . P 8 HOH BBB 89 389 69 HOH HOH . P 8 HOH BBB 90 390 54 HOH HOH . P 8 HOH BBB 91 391 134 HOH HOH . P 8 HOH BBB 92 392 130 HOH HOH . P 8 HOH BBB 93 393 43 HOH HOH . P 8 HOH BBB 94 394 39 HOH HOH . P 8 HOH BBB 95 395 56 HOH HOH . P 8 HOH BBB 96 396 129 HOH HOH . P 8 HOH BBB 97 397 117 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 GOL . . . I 3 -8.825 22.732 -17.516 1 29.66 0 C1 GOL 207 AAA 1 HETATM 2 O O1 GOL . . . I 3 -7.659 22.354 -18.228 1 27.25 0 O1 GOL 207 AAA 1 HETATM 3 C C2 GOL . . . I 3 -9.813 23.379 -18.452 1 35.99 0 C2 GOL 207 AAA 1 HETATM 4 O O2 GOL . . . I 3 -9.95 24.749 -18.115 1 37.32 0 O2 GOL 207 AAA 1 HETATM 5 C C3 GOL . . . I 3 -9.423 23.271 -19.909 1 43.61 0 C3 GOL 207 AAA 1 HETATM 6 O O3 GOL . . . I 3 -8.234 24.004 -20.194 1 45.21 0 O3 GOL 207 AAA 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #