data_7D3A # _model_server_result.job_id fg_uZKGOt61N6AR58-7DEQ _model_server_result.datetime_utc '2024-11-08 13:42:26' _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 7d3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 7D3A # _exptl.entry_id 7D3A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 270.237 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one _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 90 _cell.entry_id 7D3A _cell.length_a 63.969 _cell.length_b 63.969 _cell.length_c 192.262 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D3A _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 216 A CYS 216 1_555 A SG CYS 219 A CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? disulf ? disulf2 A SG CYS 219 A CYS 219 1_555 A SG CYS 233 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? disulf ? disulf3 A SG CYS 219 A CYS 219 1_555 A SG CYS 236 A CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? covale ? covale1 A C MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C GLY 9 A GLY 9 1_555 A N MSE 10 A MSE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale3 A C MSE 10 A MSE 10 1_555 A N ARG 11 A ARG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C GLY 17 A GLY 17 1_555 A N MSE 18 A MSE 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C MSE 18 A MSE 18 1_555 A N CYS 19 A CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale6 A C LEU 23 A LEU 23 1_555 A N MSE 24 A MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C MSE 24 A MSE 24 1_555 A N GLY 25 A GLY 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C GLU 28 A GLU 28 1_555 A N MSE 29 A MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C MSE 29 A MSE 29 1_555 A N GLY 30 A GLY 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale10 A C LYS 76 A LYS 76 1_555 A N MSE 77 A MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale11 A C MSE 77 A MSE 77 1_555 A N LEU 78 A LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale12 A C ARG 108 A ARG 108 1_555 A N MSE 109 A MSE 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 A C MSE 109 A MSE 109 1_555 A N ASP 110 A ASP 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale14 A C PHE 141 A PHE 141 1_555 A N MSE 142 A MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale15 A C MSE 142 A MSE 142 1_555 A N SER 143 A SER 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale16 A C GLY 158 A GLY 158 1_555 A N MSE 159 A MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale17 A C MSE 159 A MSE 159 1_555 A N LEU 160 A LEU 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 A C PRO 164 A PRO 164 1_555 A N MSE 165 A MSE 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 A C MSE 165 A MSE 165 1_555 A N TRP 166 A TRP 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale20 A C ASN 285 A ASN 285 1_555 A N MSE 286 A MSE 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale21 A C MSE 286 A MSE 286 1_555 A N GLN 287 A GLN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C15 H10 O5' _chem_comp.formula_weight 270.237 _chem_comp.id AGI _chem_comp.mon_nstd_flag . _chem_comp.name 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Apigenin # 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 CAG CAE AGI doub 1 n y CAG CAP AGI sing 2 n y CAE CAM AGI sing 3 n y CAM OAB AGI sing 4 n n CAM CAF AGI doub 5 n y CAF CAH AGI sing 6 n y CAH CAP AGI doub 7 n y CAP CAQ AGI sing 8 n n CAQ OAL AGI sing 9 n n CAQ CAJ AGI doub 10 n n OAL CAS AGI sing 11 n n CAJ CAR AGI sing 12 n n CAR OAA AGI doub 13 n n CAR CAT AGI sing 14 n n CAT CAS AGI doub 15 n y CAT CAO AGI sing 16 n y CAS CAK AGI sing 17 n y CAK CAN AGI doub 18 n y CAN OAC AGI sing 19 n n CAN CAI AGI sing 20 n y CAI CAO AGI doub 21 n y CAO OAD AGI sing 22 n n CAG HAG AGI sing 23 n n CAE HAE AGI sing 24 n n OAB HOAB AGI sing 25 n n CAF HAF AGI sing 26 n n CAH HAH AGI sing 27 n n CAJ HAJ AGI sing 28 n n CAK HAK AGI sing 29 n n OAC HOAC AGI sing 30 n n CAI HAI AGI sing 31 n n OAD HOAD AGI sing 32 n n # _atom_sites.entry_id 7D3A _atom_sites.fract_transf_matrix[1][1] 0.015633 _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] 0.015633 _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] 0.005201 _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 B 2 FMN A 1 401 309 FMN FMN . C 3 AGI A 1 402 311 AGI AGI . D 4 HOH A 1 501 24 HOH HOH . D 4 HOH A 2 502 21 HOH HOH . D 4 HOH A 3 503 4 HOH HOH . D 4 HOH A 4 504 29 HOH HOH . D 4 HOH A 5 505 31 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 20 HOH HOH . D 4 HOH A 8 508 14 HOH HOH . D 4 HOH A 9 509 10 HOH HOH . D 4 HOH A 10 510 26 HOH HOH . D 4 HOH A 11 511 22 HOH HOH . D 4 HOH A 12 512 2 HOH HOH . D 4 HOH A 13 513 35 HOH HOH . D 4 HOH A 14 514 5 HOH HOH . D 4 HOH A 15 515 18 HOH HOH . D 4 HOH A 16 516 3 HOH HOH . D 4 HOH A 17 517 7 HOH HOH . D 4 HOH A 18 518 13 HOH HOH . D 4 HOH A 19 519 37 HOH HOH . D 4 HOH A 20 520 34 HOH HOH . D 4 HOH A 21 521 8 HOH HOH . D 4 HOH A 22 522 11 HOH HOH . D 4 HOH A 23 523 1 HOH HOH . D 4 HOH A 24 524 9 HOH HOH . D 4 HOH A 25 525 17 HOH HOH . D 4 HOH A 26 526 25 HOH HOH . D 4 HOH A 27 527 28 HOH HOH . D 4 HOH A 28 528 15 HOH HOH . D 4 HOH A 29 529 12 HOH HOH . D 4 HOH A 30 530 33 HOH HOH . D 4 HOH A 31 531 32 HOH HOH . D 4 HOH A 32 532 27 HOH HOH . D 4 HOH A 33 533 19 HOH HOH . D 4 HOH A 34 534 36 HOH HOH . D 4 HOH A 35 535 16 HOH HOH . D 4 HOH A 36 536 30 HOH HOH . D 4 HOH A 37 537 23 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 CAG AGI . . . C 3 50.229 -28.853 -11.593 0 25.78 ? CAG AGI 402 A 1 HETATM 2 C CAE AGI . . . C 3 51.524 -29.037 -11.109 0 25.23 ? CAE AGI 402 A 1 HETATM 3 C CAM AGI . . . C 3 52.424 -29.923 -11.731 0 25.29 ? CAM AGI 402 A 1 HETATM 4 O OAB AGI . . . C 3 53.698 -30.15 -11.291 0 25.19 ? OAB AGI 402 A 1 HETATM 5 C CAF AGI . . . C 3 52.031 -30.627 -12.84 0 25.24 ? CAF AGI 402 A 1 HETATM 6 C CAH AGI . . . C 3 50.761 -30.439 -13.306 0 25.8 ? CAH AGI 402 A 1 HETATM 7 C CAP AGI . . . C 3 49.868 -29.558 -12.724 0 26.45 ? CAP AGI 402 A 1 HETATM 8 C CAQ AGI . . . C 3 48.595 -29.636 -13.448 0 28.99 ? CAQ AGI 402 A 1 HETATM 9 O OAL AGI . . . C 3 47.656 -30.427 -12.876 0 30.11 ? OAL AGI 402 A 1 HETATM 10 C CAJ AGI . . . C 3 48.455 -29.088 -14.701 0 29.87 ? CAJ AGI 402 A 1 HETATM 11 C CAR AGI . . . C 3 47.285 -29.282 -15.368 0 31.19 ? CAR AGI 402 A 1 HETATM 12 O OAA AGI . . . C 3 47.075 -28.793 -16.469 0 31.45 ? OAA AGI 402 A 1 HETATM 13 C CAT AGI . . . C 3 46.249 -30.09 -14.758 0 31.87 ? CAT AGI 402 A 1 HETATM 14 C CAS AGI . . . C 3 46.472 -30.675 -13.464 0 31.66 ? CAS AGI 402 A 1 HETATM 15 C CAK AGI . . . C 3 45.484 -31.451 -12.898 0 32.37 ? CAK AGI 402 A 1 HETATM 16 C CAN AGI . . . C 3 44.29 -31.655 -13.567 0 33.35 ? CAN AGI 402 A 1 HETATM 17 O OAC AGI . . . C 3 43.35 -32.404 -12.98 0 33.52 ? OAC AGI 402 A 1 HETATM 18 C CAI AGI . . . C 3 44.027 -31.112 -14.813 0 33.15 ? CAI AGI 402 A 1 HETATM 19 C CAO AGI . . . C 3 44.984 -30.333 -15.434 0 33.12 ? CAO AGI 402 A 1 HETATM 20 O OAD AGI . . . C 3 44.824 -29.78 -16.633 0 33.34 ? OAD AGI 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #