data_5HXC # _model_server_result.job_id A5F6j12NMMRmgjZsu2-HYg _model_server_result.datetime_utc '2024-11-14 17:12:27' _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 5hxc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":410}' # _entry.id 5HXC # _exptl.entry_id 5HXC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.235 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _entity.pdbx_number_of_molecules 7 _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 5HXC _cell.length_a 49.754 _cell.length_b 72.56 _cell.length_c 95.775 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HXC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 J N N ? 5 K N N ? 5 N N N ? 5 O N N ? 5 Q N N ? 5 R 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 metalc ? metalc1 A O ALA 47 A ALA 47 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A O THR 50 A THR 50 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc4 A OG SER 51 A SER 51 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc5 A OE2 GLU 54 A GLU 54 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 A OE1 GLU 54 A GLU 54 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc7 A OE2 GLU 54 A GLU 54 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc8 A OG SER 77 A SER 77 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc9 A O ILE 118 A ILE 118 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc10 A OD1 ASP 121 A ASP 121 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc11 A O GLY 122 A GLY 122 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc12 A OD2 ASP 127 A ASP 127 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc13 A O ALA 206 A ALA 206 1_555 E NA NA . A NA 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc14 A OG1 THR 209 A THR 209 1_555 E NA NA . A NA 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc15 A OG1 THR 209 A THR 209 1_555 E NA NA . A NA 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc16 A O THR 209 A THR 209 1_555 F NA NA . A NA 405 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc17 A O THR 209 A THR 209 1_555 F NA NA . A NA 405 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc18 A OG SER 210 A SER 210 1_555 E NA NA . A NA 404 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc19 A OE2 GLU 213 A GLU 213 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc20 A OE1 GLU 213 A GLU 213 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc21 A OE2 GLU 213 A GLU 213 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc22 A OG SER 236 A SER 236 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc23 B CA CA . A CA 401 1_555 S O25 OLC . A OLC 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc24 B CA CA . A CA 401 1_555 V O HOH . A HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? # _chem_comp.formula 'C15 H10 O8' _chem_comp.formula_weight 318.235 _chem_comp.id MYC _chem_comp.mon_nstd_flag . _chem_comp.name 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE;3,3',4',5,5',7-HEXAHYDROXYFLAVONE;MYRICETIN;CANNABISCETIN" # 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 MYC doub 274 n y C1 C6 MYC sing 275 n y C1 H1 MYC sing 276 n n C2 C3 MYC sing 277 n y C2 O30 MYC sing 278 n n C3 C4 MYC doub 279 n y C3 C9 MYC sing 280 n y C4 C5 MYC sing 281 n y C4 O12 MYC sing 282 n y C5 C6 MYC doub 283 n y C5 H5 MYC sing 284 n n C6 O29 MYC sing 285 n n C9 C10 MYC sing 286 n y C9 O13 MYC doub 287 n n C10 C11 MYC doub 288 n y C10 O27 MYC sing 289 n n C11 C14 MYC sing 290 n y C11 O12 MYC sing 291 n y C14 C15 MYC doub 292 n y C14 C19 MYC sing 293 n y C15 C16 MYC sing 294 n y C15 H15 MYC sing 295 n n C16 C17 MYC doub 296 n y C16 O25 MYC sing 297 n n C17 C18 MYC sing 298 n y C17 O24 MYC sing 299 n n C18 C19 MYC doub 300 n y C18 O23 MYC sing 301 n n C19 H19 MYC sing 302 n n O23 HO3 MYC sing 303 n n O24 HO4 MYC sing 304 n n O25 HO5 MYC sing 305 n n O27 HO7 MYC sing 306 n n O29 HO9 MYC sing 307 n n O30 HO0 MYC sing 308 n n # _atom_sites.entry_id 5HXC _atom_sites.fract_transf_matrix[1][1] 0.020099 _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] 0.013782 _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] 0.010441 _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 CA A 1 401 2 CA CA . C 2 CA A 1 402 3 CA CA . D 3 NA A 1 403 2 NA NA . E 3 NA A 1 404 3 NA NA . F 3 NA A 1 405 4 NA NA . G 4 1PE A 1 406 5 1PE PEG . H 4 1PE A 1 407 8 1PE PEG . I 5 MYC A 1 408 1 MYC FAT . J 5 MYC A 1 409 4 MYC FAT . K 5 MYC A 1 410 11 MYC FAT . L 6 MYS A 1 411 12 MYS FAT . M 6 MYS A 1 412 14 MYS FAT . N 5 MYC A 1 413 15 MYC FAT . O 5 MYC A 1 414 16 MYC FAT . P 6 MYS A 1 415 20 MYS FAT . Q 5 MYC A 1 416 21 MYC FAT . R 5 MYC A 1 417 22 MYC FAT . S 7 OLC A 1 418 3 OLC MON . T 7 OLC A 1 419 4 OLC MON . U 7 OLC A 1 420 5 OLC MON . V 8 HOH A 1 501 15 HOH HOH . V 8 HOH A 2 502 16 HOH HOH . V 8 HOH A 3 503 67 HOH HOH . V 8 HOH A 4 504 8 HOH HOH . V 8 HOH A 5 505 3 HOH HOH . V 8 HOH A 6 506 6 HOH HOH . V 8 HOH A 7 507 7 HOH HOH . V 8 HOH A 8 508 38 HOH HOH . V 8 HOH A 9 509 52 HOH HOH . V 8 HOH A 10 510 48 HOH HOH . V 8 HOH A 11 511 57 HOH HOH . V 8 HOH A 12 512 50 HOH HOH . V 8 HOH A 13 513 17 HOH HOH . V 8 HOH A 14 514 10 HOH HOH . V 8 HOH A 15 515 55 HOH HOH . V 8 HOH A 16 516 66 HOH HOH . V 8 HOH A 17 517 36 HOH HOH . V 8 HOH A 18 518 14 HOH HOH . V 8 HOH A 19 519 23 HOH HOH . V 8 HOH A 20 520 19 HOH HOH . V 8 HOH A 21 521 11 HOH HOH . V 8 HOH A 22 522 54 HOH HOH . V 8 HOH A 23 523 24 HOH HOH . V 8 HOH A 24 524 58 HOH HOH . V 8 HOH A 25 525 27 HOH HOH . V 8 HOH A 26 526 1 HOH HOH . V 8 HOH A 27 527 22 HOH HOH . V 8 HOH A 28 528 21 HOH HOH . V 8 HOH A 29 529 4 HOH HOH . V 8 HOH A 30 530 60 HOH HOH . V 8 HOH A 31 531 61 HOH HOH . V 8 HOH A 32 532 9 HOH HOH . V 8 HOH A 33 533 68 HOH HOH . V 8 HOH A 34 534 51 HOH HOH . V 8 HOH A 35 535 13 HOH HOH . V 8 HOH A 36 536 18 HOH HOH . V 8 HOH A 37 537 35 HOH HOH . V 8 HOH A 38 538 12 HOH HOH . V 8 HOH A 39 539 40 HOH HOH . V 8 HOH A 40 540 28 HOH HOH . V 8 HOH A 41 541 2 HOH HOH . V 8 HOH A 42 542 44 HOH HOH . V 8 HOH A 43 543 30 HOH HOH . V 8 HOH A 44 544 49 HOH HOH . V 8 HOH A 45 545 5 HOH HOH . V 8 HOH A 46 546 45 HOH HOH . V 8 HOH A 47 547 53 HOH HOH . V 8 HOH A 48 548 34 HOH HOH . V 8 HOH A 49 549 42 HOH HOH . V 8 HOH A 50 550 20 HOH HOH . V 8 HOH A 51 551 39 HOH HOH . V 8 HOH A 52 552 29 HOH HOH . V 8 HOH A 53 553 59 HOH HOH . V 8 HOH A 54 554 56 HOH HOH . V 8 HOH A 55 555 41 HOH HOH . V 8 HOH A 56 556 32 HOH HOH . V 8 HOH A 57 557 25 HOH HOH . V 8 HOH A 58 558 65 HOH HOH . V 8 HOH A 59 559 63 HOH HOH . V 8 HOH A 60 560 43 HOH HOH . V 8 HOH A 61 561 64 HOH HOH . V 8 HOH A 62 562 46 HOH HOH . V 8 HOH A 63 563 62 HOH HOH . V 8 HOH A 64 564 47 HOH HOH . V 8 HOH A 65 565 37 HOH HOH . V 8 HOH A 66 566 26 HOH HOH . V 8 HOH A 67 567 31 HOH HOH . V 8 HOH A 68 568 33 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 MYC . . . K 5 -8.567 4.322 20.648 1 49.06 ? C2 MYC 410 A 1 HETATM 2 C C3 MYC . . . K 5 -8.914 5.371 19.584 1 48.8 ? C3 MYC 410 A 1 HETATM 3 C C9 MYC . . . K 5 -7.662 6.138 19.124 1 33.54 ? C9 MYC 410 A 1 HETATM 4 C C10 MYC . . . K 5 -6.643 5.161 18.522 1 45.14 ? C10 MYC 410 A 1 HETATM 5 C C11 MYC . . . K 5 -5.372 5.903 18.074 1 42.88 ? C11 MYC 410 A 1 HETATM 6 C C14 MYC . . . K 5 -4.344 4.919 17.483 1 34.89 ? C14 MYC 410 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #