data_8GKN # _model_server_result.job_id D_4Fp_jgQuvwTBPGsY9QAA _model_server_result.datetime_utc '2024-11-19 13:33:34' _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 8gkn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 8GKN # _exptl.entry_id 8GKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.253 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NARINGENIN _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 8GKN _cell.length_a 89.728 _cell.length_b 167.566 _cell.length_c 63.108 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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,G 1 1 B,E,F,H 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 F N N # _chem_comp.formula 'C15 H12 O5' _chem_comp.formula_weight 272.253 _chem_comp.id NAR _chem_comp.mon_nstd_flag . _chem_comp.name NARINGENIN _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 NAR doub 237 n y C1 C6 NAR sing 238 n y C1 H11 NAR sing 239 n n C2 C3 NAR sing 240 n y C2 O4 NAR sing 241 n n C3 C4 NAR doub 242 n y C3 H31 NAR sing 243 n n C4 C5 NAR sing 244 n y C4 O5 NAR sing 245 n n C5 C6 NAR doub 246 n y C5 C7 NAR sing 247 n n C6 O1 NAR sing 248 n n C7 C8 NAR sing 249 n n C7 O2 NAR doub 250 n n C8 C9 NAR sing 251 n n C8 H81 NAR sing 252 n n C8 H82 NAR sing 253 n n C9 O1 NAR sing 254 n n C9 C10 NAR sing 255 n n C9 H9 NAR sing 256 n n C10 C11 NAR sing 257 n y C10 C15 NAR doub 258 n y C11 C12 NAR doub 259 n y C11 H111 NAR sing 260 n n C12 C13 NAR sing 261 n y C12 H121 NAR sing 262 n n C13 C14 NAR doub 263 n y C13 O3 NAR sing 264 n n C14 C15 NAR sing 265 n y C14 H141 NAR sing 266 n n C15 H151 NAR sing 267 n n O3 HO3 NAR sing 268 n n O4 H41 NAR sing 269 n n O5 H51 NAR sing 270 n n # _atom_sites.entry_id 8GKN _atom_sites.fract_transf_matrix[1][1] 0.011145 _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] 0.005968 _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] 0.015846 _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 UDP A 1 501 502 UDP UDP . D 3 NAR A 1 502 503 NAR NAR . E 2 UDP B 1 501 501 UDP UDP . F 3 NAR B 1 502 502 NAR NAR . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 57 HOH HOH . G 4 HOH A 3 603 24 HOH HOH . G 4 HOH A 4 604 266 HOH HOH . G 4 HOH A 5 605 31 HOH HOH . G 4 HOH A 6 606 5 HOH HOH . G 4 HOH A 7 607 64 HOH HOH . G 4 HOH A 8 608 112 HOH HOH . G 4 HOH A 9 609 37 HOH HOH . G 4 HOH A 10 610 45 HOH HOH . G 4 HOH A 11 611 2 HOH HOH . G 4 HOH A 12 612 60 HOH HOH . G 4 HOH A 13 613 7 HOH HOH . G 4 HOH A 14 614 135 HOH HOH . G 4 HOH A 15 615 281 HOH HOH . G 4 HOH A 16 616 19 HOH HOH . G 4 HOH A 17 617 108 HOH HOH . G 4 HOH A 18 618 191 HOH HOH . G 4 HOH A 19 619 74 HOH HOH . G 4 HOH A 20 620 274 HOH HOH . G 4 HOH A 21 621 226 HOH HOH . G 4 HOH A 22 622 11 HOH HOH . G 4 HOH A 23 623 189 HOH HOH . G 4 HOH A 24 624 51 HOH HOH . G 4 HOH A 25 625 197 HOH HOH . G 4 HOH A 26 626 6 HOH HOH . G 4 HOH A 27 627 169 HOH HOH . G 4 HOH A 28 628 103 HOH HOH . G 4 HOH A 29 629 8 HOH HOH . G 4 HOH A 30 630 127 HOH HOH . G 4 HOH A 31 631 96 HOH HOH . G 4 HOH A 32 632 137 HOH HOH . G 4 HOH A 33 633 192 HOH HOH . G 4 HOH A 34 634 239 HOH HOH . G 4 HOH A 35 635 263 HOH HOH . G 4 HOH A 36 636 133 HOH HOH . G 4 HOH A 37 637 36 HOH HOH . G 4 HOH A 38 638 20 HOH HOH . G 4 HOH A 39 639 101 HOH HOH . G 4 HOH A 40 640 220 HOH HOH . G 4 HOH A 41 641 292 HOH HOH . G 4 HOH A 42 642 188 HOH HOH . G 4 HOH A 43 643 203 HOH HOH . G 4 HOH A 44 644 22 HOH HOH . G 4 HOH A 45 645 59 HOH HOH . G 4 HOH A 46 646 61 HOH HOH . G 4 HOH A 47 647 109 HOH HOH . G 4 HOH A 48 648 54 HOH HOH . G 4 HOH A 49 649 159 HOH HOH . G 4 HOH A 50 650 13 HOH HOH . G 4 HOH A 51 651 75 HOH HOH . G 4 HOH A 52 652 35 HOH HOH . G 4 HOH A 53 653 32 HOH HOH . G 4 HOH A 54 654 204 HOH HOH . G 4 HOH A 55 655 206 HOH HOH . G 4 HOH A 56 656 50 HOH HOH . G 4 HOH A 57 657 83 HOH HOH . G 4 HOH A 58 658 39 HOH HOH . G 4 HOH A 59 659 44 HOH HOH . G 4 HOH A 60 660 79 HOH HOH . G 4 HOH A 61 661 273 HOH HOH . G 4 HOH A 62 662 76 HOH HOH . G 4 HOH A 63 663 42 HOH HOH . G 4 HOH A 64 664 194 HOH HOH . G 4 HOH A 65 665 78 HOH HOH . G 4 HOH A 66 666 186 HOH HOH . G 4 HOH A 67 667 196 HOH HOH . G 4 HOH A 68 668 111 HOH HOH . G 4 HOH A 69 669 215 HOH HOH . G 4 HOH A 70 670 68 HOH HOH . G 4 HOH A 71 671 277 HOH HOH . G 4 HOH A 72 672 193 HOH HOH . G 4 HOH A 73 673 106 HOH HOH . G 4 HOH A 74 674 211 HOH HOH . G 4 HOH A 75 675 218 HOH HOH . G 4 HOH A 76 676 210 HOH HOH . G 4 HOH A 77 677 275 HOH HOH . G 4 HOH A 78 678 67 HOH HOH . G 4 HOH A 79 679 244 HOH HOH . G 4 HOH A 80 680 251 HOH HOH . G 4 HOH A 81 681 187 HOH HOH . G 4 HOH A 82 682 209 HOH HOH . G 4 HOH A 83 683 248 HOH HOH . G 4 HOH A 84 684 205 HOH HOH . G 4 HOH A 85 685 185 HOH HOH . G 4 HOH A 86 686 243 HOH HOH . G 4 HOH A 87 687 214 HOH HOH . H 4 HOH B 1 601 56 HOH HOH . H 4 HOH B 2 602 49 HOH HOH . H 4 HOH B 3 603 285 HOH HOH . H 4 HOH B 4 604 176 HOH HOH . H 4 HOH B 5 605 28 HOH HOH . H 4 HOH B 6 606 117 HOH HOH . H 4 HOH B 7 607 4 HOH HOH . H 4 HOH B 8 608 3 HOH HOH . H 4 HOH B 9 609 114 HOH HOH . H 4 HOH B 10 610 18 HOH HOH . H 4 HOH B 11 611 97 HOH HOH . H 4 HOH B 12 612 17 HOH HOH . H 4 HOH B 13 613 38 HOH HOH . H 4 HOH B 14 614 170 HOH HOH . H 4 HOH B 15 615 175 HOH HOH . H 4 HOH B 16 616 21 HOH HOH . H 4 HOH B 17 617 207 HOH HOH . H 4 HOH B 18 618 14 HOH HOH . H 4 HOH B 19 619 52 HOH HOH . H 4 HOH B 20 620 15 HOH HOH . H 4 HOH B 21 621 95 HOH HOH . H 4 HOH B 22 622 174 HOH HOH . H 4 HOH B 23 623 12 HOH HOH . H 4 HOH B 24 624 267 HOH HOH . H 4 HOH B 25 625 91 HOH HOH . H 4 HOH B 26 626 16 HOH HOH . H 4 HOH B 27 627 173 HOH HOH . H 4 HOH B 28 628 200 HOH HOH . H 4 HOH B 29 629 283 HOH HOH . H 4 HOH B 30 630 171 HOH HOH . H 4 HOH B 31 631 89 HOH HOH . H 4 HOH B 32 632 172 HOH HOH . H 4 HOH B 33 633 298 HOH HOH . H 4 HOH B 34 634 264 HOH HOH . H 4 HOH B 35 635 125 HOH HOH . H 4 HOH B 36 636 48 HOH HOH . H 4 HOH B 37 637 261 HOH HOH . H 4 HOH B 38 638 296 HOH HOH . H 4 HOH B 39 639 282 HOH HOH . H 4 HOH B 40 640 294 HOH HOH . H 4 HOH B 41 641 178 HOH HOH . H 4 HOH B 42 642 299 HOH HOH . H 4 HOH B 43 643 293 HOH HOH . H 4 HOH B 44 644 295 HOH HOH . H 4 HOH B 45 645 297 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 NAR . . . D 3 -28.171 -14.568 -29.529 1 69.51 0 C1 NAR 502 A 1 HETATM 2 C C2 NAR . . . D 3 -27.887 -13.217 -29.667 1 78.96 0 C2 NAR 502 A 1 HETATM 3 C C3 NAR . . . D 3 -28.429 -12.46 -30.703 1 75.07 0 C3 NAR 502 A 1 HETATM 4 C C4 NAR . . . D 3 -29.267 -13.051 -31.622 1 74.18 0 C4 NAR 502 A 1 HETATM 5 C C5 NAR . . . D 3 -29.568 -14.436 -31.521 1 72.73 0 C5 NAR 502 A 1 HETATM 6 C C6 NAR . . . D 3 -28.969 -15.167 -30.479 1 72.88 0 C6 NAR 502 A 1 HETATM 7 C C7 NAR . . . D 3 -30.426 -15.089 -32.495 1 74.67 0 C7 NAR 502 A 1 HETATM 8 C C8 NAR . . . D 3 -30.789 -16.506 -32.138 1 68.79 0 C8 NAR 502 A 1 HETATM 9 C C9 NAR . . . D 3 -29.591 -17.219 -31.538 1 61.45 0 C9 NAR 502 A 1 HETATM 10 O O1 NAR . . . D 3 -29.156 -16.518 -30.328 1 66.47 0 O1 NAR 502 A 1 HETATM 11 O O2 NAR . . . D 3 -30.865 -14.527 -33.519 1 91.89 0 O2 NAR 502 A 1 HETATM 12 C C10 NAR . . . D 3 -28.454 -17.412 -32.519 1 49.2 0 C10 NAR 502 A 1 HETATM 13 C C11 NAR . . . D 3 -28.708 -17.521 -33.878 1 43.44 0 C11 NAR 502 A 1 HETATM 14 C C12 NAR . . . D 3 -27.692 -17.728 -34.8 1 43.47 0 C12 NAR 502 A 1 HETATM 15 C C13 NAR . . . D 3 -26.374 -17.872 -34.388 1 42.71 0 C13 NAR 502 A 1 HETATM 16 C C14 NAR . . . D 3 -26.105 -17.803 -33.033 1 42.06 0 C14 NAR 502 A 1 HETATM 17 C C15 NAR . . . D 3 -27.132 -17.571 -32.117 1 48.76 0 C15 NAR 502 A 1 HETATM 18 O O3 NAR . . . D 3 -25.383 -18.101 -35.352 1 40.24 0 O3 NAR 502 A 1 HETATM 19 O O4 NAR . . . D 3 -27.063 -12.597 -28.757 1 94.23 0 O4 NAR 502 A 1 HETATM 20 O O5 NAR . . . D 3 -29.842 -12.333 -32.676 1 62.76 0 O5 NAR 502 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 867 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 20 #