data_7D38 # _model_server_result.job_id Haes8XhD_DZyYbJwvqnOhQ _model_server_result.datetime_utc '2024-11-08 21:04:27' _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 7d38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7D38 # _exptl.entry_id 7D38 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 254.237 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description chrysin _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 7D38 _cell.length_a 66.365 _cell.length_b 66.365 _cell.length_c 194.057 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D38 _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 2 _struct_asym.id B _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 219 A CYS 219 1_555 A SG CYS 233 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 219 A CYS 219 1_555 A SG CYS 236 A CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A C MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C GLY 9 A GLY 9 1_555 A N MSE 10 A MSE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale3 A C MSE 10 A MSE 10 1_555 A N ARG 11 A ARG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale4 A C GLY 17 A GLY 17 1_555 A N MSE 18 A MSE 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C MSE 18 A MSE 18 1_555 A N CYS 19 A CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale6 A C LEU 23 A LEU 23 1_555 A N MSE 24 A MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C MSE 24 A MSE 24 1_555 A N GLY 25 A GLY 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 A C GLU 28 A GLU 28 1_555 A N MSE 29 A MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 A C MSE 29 A MSE 29 1_555 A N GLY 30 A GLY 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C LYS 76 A LYS 76 1_555 A N MSE 77 A MSE 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C MSE 77 A MSE 77 1_555 A N LEU 78 A LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale12 A C ARG 108 A ARG 108 1_555 A N MSE 109 A MSE 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 A C MSE 109 A MSE 109 1_555 A N ASP 110 A ASP 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale14 A C PHE 141 A PHE 141 1_555 A N MSE 142 A MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 A C MSE 142 A MSE 142 1_555 A N SER 143 A SER 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale16 A C GLY 158 A GLY 158 1_555 A N MSE 159 A MSE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 A C MSE 165 A MSE 165 1_555 A N TRP 166 A TRP 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale20 A C ASN 285 A ASN 285 1_555 A N MSE 286 A MSE 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale21 A C MSE 286 A MSE 286 1_555 A N GLN 287 A GLN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _chem_comp.formula 'C15 H10 O4' _chem_comp.formula_weight 254.237 _chem_comp.id 57D _chem_comp.mon_nstd_flag . _chem_comp.name chrysin _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5,7-dihydroxy-2-phenyl-4H-chromen-4-one # 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 C2 C3 57D doub 1 n n C2 O1 57D sing 2 n n C2 C1' 57D sing 3 n n C3 C4 57D sing 4 n n C4 C5 57D sing 5 n n C4 O4 57D doub 6 n n C5 C6 57D doub 7 n y C5 C10 57D sing 8 n y C6 C7 57D sing 9 n y C6 O5 57D sing 10 n n C7 C8 57D doub 11 n y C8 C9 57D sing 12 n y C8 O7 57D sing 13 n n C9 C10 57D doub 14 n y C10 O1 57D sing 15 n n C2' C3' 57D doub 16 n y C2' C1' 57D sing 17 n y C3' C4' 57D sing 18 n y C4' C5' 57D doub 19 n y C5' C6' 57D sing 20 n y C6' C1' 57D doub 21 n y C3 H3 57D sing 22 n n C7 H7 57D sing 23 n n C9 H9 57D sing 24 n n O5 HO5 57D sing 25 n n O7 HO7 57D sing 26 n n C2' H2' 57D sing 27 n n C3' H3' 57D sing 28 n n C4' H4' 57D sing 29 n n C5' H5' 57D sing 30 n n C6' H6' 57D sing 31 n n # _atom_sites.entry_id 7D38 _atom_sites.fract_transf_matrix[1][1] 0.015068 _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] 0.015068 _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] 0.005153 _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 57D A 1 401 309 57D 57D . C 3 FMN A 1 402 310 FMN FMN . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 26 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 30 HOH HOH . D 4 HOH A 5 505 16 HOH HOH . D 4 HOH A 6 506 20 HOH HOH . D 4 HOH A 7 507 9 HOH HOH . D 4 HOH A 8 508 10 HOH HOH . D 4 HOH A 9 509 7 HOH HOH . D 4 HOH A 10 510 19 HOH HOH . D 4 HOH A 11 511 31 HOH HOH . D 4 HOH A 12 512 15 HOH HOH . D 4 HOH A 13 513 27 HOH HOH . D 4 HOH A 14 514 23 HOH HOH . D 4 HOH A 15 515 2 HOH HOH . D 4 HOH A 16 516 4 HOH HOH . D 4 HOH A 17 517 28 HOH HOH . D 4 HOH A 18 518 12 HOH HOH . D 4 HOH A 19 519 5 HOH HOH . D 4 HOH A 20 520 24 HOH HOH . D 4 HOH A 21 521 17 HOH HOH . D 4 HOH A 22 522 11 HOH HOH . D 4 HOH A 23 523 14 HOH HOH . D 4 HOH A 24 524 6 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 13 HOH HOH . D 4 HOH A 27 527 21 HOH HOH . D 4 HOH A 28 528 22 HOH HOH . D 4 HOH A 29 529 18 HOH HOH . D 4 HOH A 30 530 8 HOH HOH . D 4 HOH A 31 531 32 HOH HOH . D 4 HOH A 32 532 29 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 C2 57D . . . B 2 -17.326 -3.913 -14.011 0 37.77 ? C2 57D 401 A 1 HETATM 2 C C3 57D . . . B 2 -17.255 -4.54 -15.027 0 34.38 ? C3 57D 401 A 1 HETATM 3 C C4 57D . . . B 2 -16.146 -4.638 -15.793 0 31.73 ? C4 57D 401 A 1 HETATM 4 C C5 57D . . . B 2 -14.929 -3.836 -15.238 0 29.53 ? C5 57D 401 A 1 HETATM 5 C C6 57D . . . B 2 -13.654 -3.78 -15.862 0 27.95 ? C6 57D 401 A 1 HETATM 6 C C7 57D . . . B 2 -12.565 -2.963 -15.212 0 26.61 ? C7 57D 401 A 1 HETATM 7 C C8 57D . . . B 2 -12.837 -2.247 -13.959 0 25.04 ? C8 57D 401 A 1 HETATM 8 C C9 57D . . . B 2 -14.06 -2.336 -13.413 0 26.73 ? C9 57D 401 A 1 HETATM 9 C C10 57D . . . B 2 -14.926 -3.033 -14.004 0 29.91 ? C10 57D 401 A 1 HETATM 10 O O1 57D . . . B 2 -16.343 -3.185 -13.448 0 33.36 ? O1 57D 401 A 1 HETATM 11 O O4 57D . . . B 2 -16.093 -5.386 -16.975 0 31.12 ? O4 57D 401 A 1 HETATM 12 O O5 57D . . . B 2 -13.407 -4.467 -17.057 0 28.54 ? O5 57D 401 A 1 HETATM 13 O O7 57D . . . B 2 -11.842 -1.483 -13.337 0 23.72 ? O7 57D 401 A 1 HETATM 14 C C2' 57D . . . B 2 -18.666 -4.399 -11.79 0 49.17 ? C2' 57D 401 A 1 HETATM 15 C C3' 57D . . . B 2 -19.78 -4.325 -11.093 0 51.13 ? C3' 57D 401 A 1 HETATM 16 C C4' 57D . . . B 2 -21.019 -3.676 -11.707 0 51.77 ? C4' 57D 401 A 1 HETATM 17 C C5' 57D . . . B 2 -20.975 -3.191 -12.931 0 50.56 ? C5' 57D 401 A 1 HETATM 18 C C6' 57D . . . B 2 -19.684 -3.277 -13.739 0 48.61 ? C6' 57D 401 A 1 HETATM 19 C C1' 57D . . . B 2 -18.623 -3.851 -13.214 0 45.25 ? C1' 57D 401 A 1 HETATM 20 H H3 57D . . . B 2 -17.955 -4.961 -15.284 0 41.26 ? H3 57D 401 A 1 HETATM 21 H H7 57D . . . B 2 -11.724 -2.914 -15.603 0 31.93 ? H7 57D 401 A 1 HETATM 22 H H9 57D . . . B 2 -14.263 -1.894 -12.621 0 32.08 ? H9 57D 401 A 1 HETATM 23 H HO5 57D . . . B 2 -13.25 -3.92 -17.664 0 34.25 ? HO5 57D 401 A 1 HETATM 24 H HO7 57D . . . B 2 -11.684 -0.808 -13.796 0 28.46 ? HO7 57D 401 A 1 HETATM 25 H H2' 57D . . . B 2 -17.91 -4.794 -11.419 0 59.01 ? H2' 57D 401 A 1 HETATM 26 H H3' 57D . . . B 2 -19.813 -4.669 -10.229 0 61.35 ? H3' 57D 401 A 1 HETATM 27 H H4' 57D . . . B 2 -21.807 -3.626 -11.217 0 62.12 ? H4' 57D 401 A 1 HETATM 28 H H5' 57D . . . B 2 -21.731 -2.798 -13.303 0 60.68 ? H5' 57D 401 A 1 HETATM 29 H H6' 57D . . . B 2 -19.65 -2.936 -14.603 0 58.33 ? H6' 57D 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #