data_2ZVJ # _model_server_result.job_id VMPCqnGgCNPST_SdEw7-kg _model_server_result.datetime_utc '2025-01-02 16:04:52' _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 2zvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 2ZVJ # _exptl.entry_id 2ZVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 254.237 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 7,8-dihydroxy-4-phenyl-2H-chromen-2-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 120 _cell.entry_id 2ZVJ _cell.length_a 50.448 _cell.length_b 50.448 _cell.length_c 167.626 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZVJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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,E _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 4 _struct_asym.id D _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 metalc ? metalc1 A OD2 ASP 143 A ASP 141 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc2 A OD2 ASP 171 A ASP 169 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc3 A OD1 ASN 172 A ASN 170 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc4 B MG MG . A MG 300 1_555 D O9 KOM . A KOM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc5 B MG MG . A MG 300 1_555 D O10 KOM . A KOM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc6 B MG MG . A MG 300 1_555 E O HOH . A HOH 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? # _chem_comp.formula 'C15 H10 O4' _chem_comp.formula_weight 254.237 _chem_comp.id KOM _chem_comp.mon_nstd_flag . _chem_comp.name 7,8-dihydroxy-4-phenyl-2H-chromen-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-phenyl-7,8-dihydroxycoumarine # 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 O15 C13 KOM doub 173 n n C13 O14 KOM sing 174 n n C13 C12 KOM sing 175 n n O14 C4 KOM sing 176 n n C4 C5 KOM doub 177 n y C4 C3 KOM sing 178 n y C5 O9 KOM sing 179 n n C5 C6 KOM sing 180 n y C6 O10 KOM sing 181 n n C6 C1 KOM doub 182 n y C1 C2 KOM sing 183 n y C12 C11 KOM doub 184 n n C11 C3 KOM sing 185 n n C11 C18 KOM sing 186 n n C3 C2 KOM doub 187 n y C18 C24 KOM doub 188 n y C18 C20 KOM sing 189 n y C24 C23 KOM sing 190 n y C23 C22 KOM doub 191 n y C22 C21 KOM sing 192 n y C21 C20 KOM doub 193 n y O9 HO9 KOM sing 194 n n O10 HO10 KOM sing 195 n n C1 H1 KOM sing 196 n n C12 H12 KOM sing 197 n n C2 H2 KOM sing 198 n n C24 H24 KOM sing 199 n n C23 H23 KOM sing 200 n n C22 H22 KOM sing 201 n n C21 H21 KOM sing 202 n n C20 H20 KOM sing 203 n n # _atom_sites.entry_id 2ZVJ _atom_sites.fract_transf_matrix[1][1] 0.019822 _atom_sites.fract_transf_matrix[1][2] 0.011444 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022889 _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] 0.005966 _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 MG A 1 300 300 MG MG . C 3 SAM A 1 301 301 SAM SAM . D 4 KOM A 1 302 302 KOM KOM . E 5 HOH A 1 303 303 HOH HOH . E 5 HOH A 2 304 304 HOH HOH . E 5 HOH A 3 305 305 HOH HOH . E 5 HOH A 4 306 306 HOH HOH . E 5 HOH A 5 307 307 HOH HOH . E 5 HOH A 6 308 308 HOH HOH . E 5 HOH A 7 309 309 HOH HOH . E 5 HOH A 8 310 310 HOH HOH . E 5 HOH A 9 311 311 HOH HOH . E 5 HOH A 10 312 312 HOH HOH . E 5 HOH A 11 313 313 HOH HOH . E 5 HOH A 12 314 314 HOH HOH . E 5 HOH A 13 315 315 HOH HOH . E 5 HOH A 14 316 316 HOH HOH . E 5 HOH A 15 317 317 HOH HOH . E 5 HOH A 16 318 318 HOH HOH . E 5 HOH A 17 319 319 HOH HOH . E 5 HOH A 18 320 320 HOH HOH . E 5 HOH A 19 321 321 HOH HOH . E 5 HOH A 20 322 322 HOH HOH . E 5 HOH A 21 323 323 HOH HOH . E 5 HOH A 22 324 324 HOH HOH . E 5 HOH A 23 325 325 HOH HOH . E 5 HOH A 24 326 326 HOH HOH . E 5 HOH A 25 327 327 HOH HOH . E 5 HOH A 26 328 328 HOH HOH . E 5 HOH A 27 329 329 HOH HOH . E 5 HOH A 28 330 330 HOH HOH . E 5 HOH A 29 331 331 HOH HOH . E 5 HOH A 30 332 332 HOH HOH . E 5 HOH A 31 333 333 HOH HOH . E 5 HOH A 32 334 334 HOH HOH . E 5 HOH A 33 335 335 HOH HOH . E 5 HOH A 34 336 336 HOH HOH . E 5 HOH A 35 337 337 HOH HOH . E 5 HOH A 36 338 338 HOH HOH . E 5 HOH A 37 339 339 HOH HOH . E 5 HOH A 38 340 340 HOH HOH . E 5 HOH A 39 341 341 HOH HOH . E 5 HOH A 40 342 342 HOH HOH . E 5 HOH A 41 343 343 HOH HOH . E 5 HOH A 42 344 344 HOH HOH . E 5 HOH A 43 345 345 HOH HOH . E 5 HOH A 44 346 346 HOH HOH . E 5 HOH A 45 347 347 HOH HOH . E 5 HOH A 46 348 348 HOH HOH . E 5 HOH A 47 349 349 HOH HOH . E 5 HOH A 48 350 350 HOH HOH . E 5 HOH A 49 351 351 HOH HOH . E 5 HOH A 50 352 352 HOH HOH . E 5 HOH A 51 353 353 HOH HOH . E 5 HOH A 52 354 354 HOH HOH . E 5 HOH A 53 355 355 HOH HOH . E 5 HOH A 54 356 356 HOH HOH . E 5 HOH A 55 357 357 HOH HOH . E 5 HOH A 56 358 358 HOH HOH . E 5 HOH A 57 359 359 HOH HOH . E 5 HOH A 58 360 360 HOH HOH . E 5 HOH A 59 361 361 HOH HOH . E 5 HOH A 60 362 362 HOH HOH . E 5 HOH A 61 363 363 HOH HOH . E 5 HOH A 62 364 364 HOH HOH . E 5 HOH A 63 365 365 HOH HOH . E 5 HOH A 64 366 366 HOH HOH . E 5 HOH A 65 367 367 HOH HOH . E 5 HOH A 66 368 368 HOH HOH . E 5 HOH A 67 369 369 HOH HOH . E 5 HOH A 68 370 370 HOH HOH . E 5 HOH A 69 371 371 HOH HOH . E 5 HOH A 70 372 372 HOH HOH . E 5 HOH A 71 373 373 HOH HOH . E 5 HOH A 72 374 374 HOH HOH . E 5 HOH A 73 375 375 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 O O15 KOM . . . D 4 -12.934 2.622 -21.285 1 49.91 ? O15 KOM 302 A 1 HETATM 2 C C13 KOM . . . D 4 -12.924 3.83 -21.557 1 50.19 ? C13 KOM 302 A 1 HETATM 3 O O14 KOM . . . D 4 -14.072 4.527 -21.31 1 50.84 ? O14 KOM 302 A 1 HETATM 4 C C4 KOM . . . D 4 -14.16 5.866 -21.598 1 50.59 ? C4 KOM 302 A 1 HETATM 5 C C5 KOM . . . D 4 -15.407 6.616 -21.317 1 50.21 ? C5 KOM 302 A 1 HETATM 6 O O9 KOM . . . D 4 -16.5 6.014 -20.764 1 49.84 ? O9 KOM 302 A 1 HETATM 7 C C6 KOM . . . D 4 -15.437 8.057 -21.659 1 50.28 ? C6 KOM 302 A 1 HETATM 8 O O10 KOM . . . D 4 -16.591 8.742 -21.416 1 49.37 ? O10 KOM 302 A 1 HETATM 9 C C1 KOM . . . D 4 -14.305 8.668 -22.224 1 50.28 ? C1 KOM 302 A 1 HETATM 10 C C12 KOM . . . D 4 -11.79 4.429 -22.109 1 49.71 ? C12 KOM 302 A 1 HETATM 11 C C11 KOM . . . D 4 -11.765 5.783 -22.451 1 50.23 ? C11 KOM 302 A 1 HETATM 12 C C3 KOM . . . D 4 -12.998 6.59 -22.182 1 49.96 ? C3 KOM 302 A 1 HETATM 13 C C2 KOM . . . D 4 -13.125 7.955 -22.474 1 50.13 ? C2 KOM 302 A 1 HETATM 14 C C18 KOM . . . D 4 -10.499 6.359 -23.012 1 50.47 ? C18 KOM 302 A 1 HETATM 15 C C24 KOM . . . D 4 -9.939 7.495 -22.398 1 50.73 ? C24 KOM 302 A 1 HETATM 16 C C23 KOM . . . D 4 -8.746 8.062 -22.868 1 51.63 ? C23 KOM 302 A 1 HETATM 17 C C22 KOM . . . D 4 -8.089 7.462 -23.948 1 51.79 ? C22 KOM 302 A 1 HETATM 18 C C21 KOM . . . D 4 -8.632 6.312 -24.553 1 52.33 ? C21 KOM 302 A 1 HETATM 19 C C20 KOM . . . D 4 -9.829 5.753 -24.084 1 50.99 ? C20 KOM 302 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 50 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 19 #