data_4GD7 # _model_server_result.job_id H4T0puoDBfPgVLvq97_EKA _model_server_result.datetime_utc '2024-11-12 21:17:20' _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 4gd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4GD7 # _exptl.entry_id 4GD7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 220.178 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-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 4GD7 _cell.length_a 95.784 _cell.length_b 95.784 _cell.length_c 81.682 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GD7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # 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 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 54.454667 # _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 covale ? covale1 A C ARG 42 A ARG 42 1_555 A N CME 43 A CME 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C CME 43 A CME 43 1_555 A N GLY 44 A GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C MET 179 A MET 179 1_555 A N CME 180 A CME 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale4 A C CME 180 A CME 180 1_555 A N ALA 181 A ALA 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 A C PRO 194 A PRO 194 1_555 A N CSD 195 A CSD 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C CSD 195 A CSD 195 1_555 A N HIS 196 A HIS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? # _chem_comp.formula 'C11 H8 O5' _chem_comp.formula_weight 220.178 _chem_comp.id TIY _chem_comp.mon_nstd_flag . _chem_comp.name 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Purpurogallin # 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 C13 O14 TIY sing 355 n n C13 C12 TIY sing 356 n y C15 C13 TIY doub 357 n y O01 C02 TIY sing 358 n n C02 C15 TIY sing 359 n y C02 C03 TIY doub 360 n y C03 C04 TIY sing 361 n y C04 C12 TIY doub 362 n y C04 C05 TIY sing 363 n n C05 C06 TIY doub 364 n n C07 C06 TIY sing 365 n n C08 C07 TIY doub 366 n n C09 C03 TIY sing 367 n n C09 C08 TIY sing 368 n n O10 C09 TIY doub 369 n n O11 C08 TIY sing 370 n n O16 C15 TIY sing 371 n n O01 HO01 TIY sing 372 n n C06 H06 TIY sing 373 n n C07 H07 TIY sing 374 n n O11 H4 TIY sing 375 n n C12 H12 TIY sing 376 n n O14 HO14 TIY sing 377 n n O16 HO16 TIY sing 378 n n C05 H05 TIY sing 379 n n # _atom_sites.entry_id 4GD7 _atom_sites.fract_transf_matrix[1][1] 0.01044 _atom_sites.fract_transf_matrix[1][2] 0.006028 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012055 _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] 0.012243 _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 EDO A 1 401 314 EDO EDO . C 3 TIY A 1 402 500 TIY P67 . D 4 SO4 A 1 403 501 SO4 SO4 . E 4 SO4 A 1 404 502 SO4 SO4 . F 4 SO4 A 1 405 503 SO4 SO4 . G 5 HOH A 1 501 600 HOH HOH . G 5 HOH A 2 502 602 HOH HOH . G 5 HOH A 3 503 605 HOH HOH . G 5 HOH A 4 504 609 HOH HOH . G 5 HOH A 5 505 610 HOH HOH . G 5 HOH A 6 506 611 HOH HOH . G 5 HOH A 7 507 612 HOH HOH . G 5 HOH A 8 508 613 HOH HOH . G 5 HOH A 9 509 614 HOH HOH . G 5 HOH A 10 510 615 HOH HOH . G 5 HOH A 11 511 617 HOH HOH . G 5 HOH A 12 512 618 HOH HOH . G 5 HOH A 13 513 619 HOH HOH . G 5 HOH A 14 514 620 HOH HOH . G 5 HOH A 15 515 625 HOH HOH . G 5 HOH A 16 516 626 HOH HOH . G 5 HOH A 17 517 627 HOH HOH . G 5 HOH A 18 518 628 HOH HOH . G 5 HOH A 19 519 631 HOH HOH . G 5 HOH A 20 520 633 HOH HOH . G 5 HOH A 21 521 634 HOH HOH . G 5 HOH A 22 522 635 HOH HOH . G 5 HOH A 23 523 636 HOH HOH . G 5 HOH A 24 524 637 HOH HOH . G 5 HOH A 25 525 638 HOH HOH . G 5 HOH A 26 526 639 HOH HOH . G 5 HOH A 27 527 644 HOH HOH . G 5 HOH A 28 528 646 HOH HOH . G 5 HOH A 29 529 652 HOH HOH . G 5 HOH A 30 530 656 HOH HOH . G 5 HOH A 31 531 659 HOH HOH . G 5 HOH A 32 532 660 HOH HOH . G 5 HOH A 33 533 664 HOH HOH . G 5 HOH A 34 534 669 HOH HOH . G 5 HOH A 35 535 672 HOH HOH . G 5 HOH A 36 536 673 HOH HOH . G 5 HOH A 37 537 675 HOH HOH . G 5 HOH A 38 538 676 HOH HOH . G 5 HOH A 39 539 678 HOH HOH . G 5 HOH A 40 540 684 HOH HOH . G 5 HOH A 41 541 685 HOH HOH . G 5 HOH A 42 542 687 HOH HOH . G 5 HOH A 43 543 693 HOH HOH . G 5 HOH A 44 544 695 HOH HOH . G 5 HOH A 45 545 702 HOH HOH . G 5 HOH A 46 546 719 HOH HOH . G 5 HOH A 47 547 730 HOH HOH . G 5 HOH A 48 548 738 HOH HOH . G 5 HOH A 49 549 754 HOH HOH . G 5 HOH A 50 550 759 HOH HOH . G 5 HOH A 51 551 760 HOH HOH . G 5 HOH A 52 552 761 HOH HOH . G 5 HOH A 53 553 762 HOH HOH . G 5 HOH A 54 554 763 HOH HOH . G 5 HOH A 55 555 764 HOH HOH . G 5 HOH A 56 556 765 HOH HOH . G 5 HOH A 57 557 766 HOH HOH . G 5 HOH A 58 558 767 HOH HOH . G 5 HOH A 59 559 768 HOH HOH . G 5 HOH A 60 560 769 HOH HOH . G 5 HOH A 61 561 772 HOH HOH . G 5 HOH A 62 562 773 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 C13 TIY . . . C 3 34.424 1.889 26.406 0.25 67.95 ? C13 TIY 402 A 1 HETATM 2 C C15 TIY . . . C 3 33.073 2.101 26.164 0.25 68.04 ? C15 TIY 402 A 1 HETATM 3 O O01 TIY . . . C 3 31.142 0.264 26.744 0.25 68.26 ? O01 TIY 402 A 1 HETATM 4 C C02 TIY . . . C 3 32.576 0.827 26.674 0.25 68.03 ? C02 TIY 402 A 1 HETATM 5 C C03 TIY . . . C 3 33.625 -0.17 27.07 0.25 67.79 ? C03 TIY 402 A 1 HETATM 6 C C04 TIY . . . C 3 34.982 -0.383 27.052 0.25 67.71 ? C04 TIY 402 A 1 HETATM 7 C C05 TIY . . . C 3 35.587 -1.63 27.542 0.25 67.44 ? C05 TIY 402 A 1 HETATM 8 C C06 TIY . . . C 3 35.016 -2.819 27.656 0.25 67.24 ? C06 TIY 402 A 1 HETATM 9 C C07 TIY . . . C 3 33.685 -3.243 27.062 0.25 67.39 ? C07 TIY 402 A 1 HETATM 10 C C08 TIY . . . C 3 32.466 -2.847 27.313 0.25 67.9 ? C08 TIY 402 A 1 HETATM 11 C C09 TIY . . . C 3 32.49 -1.485 27.407 0.25 68 ? C09 TIY 402 A 1 HETATM 12 O O10 TIY . . . C 3 31.278 -1.16 27.633 0.25 68.33 ? O10 TIY 402 A 1 HETATM 13 O O11 TIY . . . C 3 31.42 -3.679 27.575 0.25 67.59 ? O11 TIY 402 A 1 HETATM 14 C C12 TIY . . . C 3 35.481 0.608 26.862 0.25 67.93 ? C12 TIY 402 A 1 HETATM 15 O O14 TIY . . . C 3 35.28 2.932 26.187 0.25 67.21 ? O14 TIY 402 A 1 HETATM 16 O O16 TIY . . . C 3 32.647 3.313 25.725 0.25 68.25 ? O16 TIY 402 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #