data_8YYP # _model_server_result.job_id Ef5-8q7LlRtLp-vnT4OV8w _model_server_result.datetime_utc '2024-11-20 10:22:06' _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 8yyp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":503}' # _entry.id 8YYP # _exptl.entry_id 8YYP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 372.42 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione _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 8YYP _cell.length_a 84.453 _cell.length_b 84.453 _cell.length_c 133.377 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YYP _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 G _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 SG CYS 361 A CYS 361 1_555 D FE HEM . A HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc2 B SG CYS 361 B CYS 361 1_555 F FE HEM . B HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? # _chem_comp.formula 'C22 H20 N4 O2' _chem_comp.formula_weight 372.42 _chem_comp.id UYM _chem_comp.mon_nstd_flag . _chem_comp.name (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C8 C9 UYM doub 456 n y C8 C7 UYM sing 457 n y C9 C10 UYM sing 458 n y C7 C6 UYM doub 459 n y C10 C5 UYM doub 460 n y C6 C5 UYM sing 461 n y C6 C3 UYM sing 462 n y C5 N UYM sing 463 n y O C UYM doub 464 n n C3 C2 UYM sing 465 n n C3 C4 UYM doub 466 n y C1 C UYM sing 467 n n C1 C2 UYM sing 468 n n C1 N1 UYM sing 469 n n N C4 UYM sing 470 n y C N2 UYM sing 471 n n N1 C15 UYM sing 472 n n N2 C11 UYM sing 473 n n C15 C11 UYM sing 474 n n C15 O1 UYM doub 475 n n C11 C12 UYM sing 476 n n C35 C34 UYM doub 477 n y C35 N36 UYM sing 478 n y C12 C34 UYM sing 479 n n C34 C38 UYM sing 480 n y N36 C37 UYM sing 481 n y C38 C37 UYM doub 482 n y C38 C39 UYM sing 483 n y C37 C42 UYM sing 484 n y C39 C40 UYM doub 485 n y C42 C41 UYM doub 486 n y C40 C41 UYM sing 487 n y N H1 UYM sing 488 n n C1 H2 UYM sing 489 n n C10 H3 UYM sing 490 n n C11 H4 UYM sing 491 n n C12 H5 UYM sing 492 n n C12 H6 UYM sing 493 n n C2 H7 UYM sing 494 n n C2 H8 UYM sing 495 n n C35 H9 UYM sing 496 n n C39 H10 UYM sing 497 n n C4 H11 UYM sing 498 n n C40 H12 UYM sing 499 n n C41 H13 UYM sing 500 n n C42 H14 UYM sing 501 n n C7 H15 UYM sing 502 n n C8 H16 UYM sing 503 n n C9 H17 UYM sing 504 n n N1 H18 UYM sing 505 n n N2 H19 UYM sing 506 n n N36 H20 UYM sing 507 n n # _atom_sites.entry_id 8YYP _atom_sites.fract_transf_matrix[1][1] 0.011841 _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] 0.011841 _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] 0.007498 _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 C 2 ADE A 1 501 501 ADE ADF . D 3 HEM A 1 502 502 HEM DRG . E 2 ADE B 1 501 501 ADE ADF . F 3 HEM B 1 502 502 HEM DRG . G 4 UYM B 1 503 504 UYM CWW . H 5 HOH A 1 601 178 HOH HOH . H 5 HOH A 2 602 173 HOH HOH . H 5 HOH A 3 603 132 HOH HOH . H 5 HOH A 4 604 133 HOH HOH . H 5 HOH A 5 605 45 HOH HOH . H 5 HOH A 6 606 39 HOH HOH . H 5 HOH A 7 607 146 HOH HOH . H 5 HOH A 8 608 105 HOH HOH . H 5 HOH A 9 609 193 HOH HOH . H 5 HOH A 10 610 151 HOH HOH . H 5 HOH A 11 611 166 HOH HOH . H 5 HOH A 12 612 21 HOH HOH . H 5 HOH A 13 613 65 HOH HOH . H 5 HOH A 14 614 55 HOH HOH . H 5 HOH A 15 615 16 HOH HOH . H 5 HOH A 16 616 74 HOH HOH . H 5 HOH A 17 617 56 HOH HOH . H 5 HOH A 18 618 128 HOH HOH . H 5 HOH A 19 619 60 HOH HOH . H 5 HOH A 20 620 112 HOH HOH . H 5 HOH A 21 621 54 HOH HOH . H 5 HOH A 22 622 85 HOH HOH . H 5 HOH A 23 623 196 HOH HOH . H 5 HOH A 24 624 47 HOH HOH . H 5 HOH A 25 625 184 HOH HOH . H 5 HOH A 26 626 191 HOH HOH . H 5 HOH A 27 627 198 HOH HOH . H 5 HOH A 28 628 19 HOH HOH . H 5 HOH A 29 629 136 HOH HOH . H 5 HOH A 30 630 165 HOH HOH . H 5 HOH A 31 631 125 HOH HOH . H 5 HOH A 32 632 64 HOH HOH . H 5 HOH A 33 633 189 HOH HOH . H 5 HOH A 34 634 26 HOH HOH . H 5 HOH A 35 635 49 HOH HOH . H 5 HOH A 36 636 11 HOH HOH . H 5 HOH A 37 637 37 HOH HOH . H 5 HOH A 38 638 180 HOH HOH . H 5 HOH A 39 639 86 HOH HOH . H 5 HOH A 40 640 154 HOH HOH . H 5 HOH A 41 641 9 HOH HOH . H 5 HOH A 42 642 8 HOH HOH . H 5 HOH A 43 643 13 HOH HOH . H 5 HOH A 44 644 28 HOH HOH . H 5 HOH A 45 645 3 HOH HOH . H 5 HOH A 46 646 195 HOH HOH . H 5 HOH A 47 647 163 HOH HOH . H 5 HOH A 48 648 91 HOH HOH . H 5 HOH A 49 649 89 HOH HOH . H 5 HOH A 50 650 135 HOH HOH . H 5 HOH A 51 651 187 HOH HOH . H 5 HOH A 52 652 186 HOH HOH . H 5 HOH A 53 653 94 HOH HOH . H 5 HOH A 54 654 36 HOH HOH . H 5 HOH A 55 655 70 HOH HOH . H 5 HOH A 56 656 68 HOH HOH . H 5 HOH A 57 657 90 HOH HOH . H 5 HOH A 58 658 161 HOH HOH . H 5 HOH A 59 659 134 HOH HOH . H 5 HOH A 60 660 62 HOH HOH . H 5 HOH A 61 661 121 HOH HOH . H 5 HOH A 62 662 41 HOH HOH . H 5 HOH A 63 663 115 HOH HOH . H 5 HOH A 64 664 174 HOH HOH . H 5 HOH A 65 665 59 HOH HOH . H 5 HOH A 66 666 131 HOH HOH . H 5 HOH A 67 667 48 HOH HOH . H 5 HOH A 68 668 43 HOH HOH . H 5 HOH A 69 669 102 HOH HOH . H 5 HOH A 70 670 172 HOH HOH . H 5 HOH A 71 671 14 HOH HOH . H 5 HOH A 72 672 181 HOH HOH . H 5 HOH A 73 673 162 HOH HOH . H 5 HOH A 74 674 30 HOH HOH . H 5 HOH A 75 675 156 HOH HOH . H 5 HOH A 76 676 153 HOH HOH . H 5 HOH A 77 677 188 HOH HOH . H 5 HOH A 78 678 99 HOH HOH . H 5 HOH A 79 679 177 HOH HOH . H 5 HOH A 80 680 144 HOH HOH . H 5 HOH A 81 681 168 HOH HOH . H 5 HOH A 82 682 110 HOH HOH . H 5 HOH A 83 683 182 HOH HOH . H 5 HOH A 84 684 97 HOH HOH . H 5 HOH A 85 685 87 HOH HOH . H 5 HOH A 86 686 175 HOH HOH . H 5 HOH A 87 687 185 HOH HOH . H 5 HOH A 88 688 117 HOH HOH . I 5 HOH B 1 601 29 HOH HOH . I 5 HOH B 2 602 5 HOH HOH . I 5 HOH B 3 603 199 HOH HOH . I 5 HOH B 4 604 22 HOH HOH . I 5 HOH B 5 605 152 HOH HOH . I 5 HOH B 6 606 4 HOH HOH . I 5 HOH B 7 607 203 HOH HOH . I 5 HOH B 8 608 126 HOH HOH . I 5 HOH B 9 609 17 HOH HOH . I 5 HOH B 10 610 52 HOH HOH . I 5 HOH B 11 611 108 HOH HOH . I 5 HOH B 12 612 92 HOH HOH . I 5 HOH B 13 613 33 HOH HOH . I 5 HOH B 14 614 61 HOH HOH . I 5 HOH B 15 615 130 HOH HOH . I 5 HOH B 16 616 109 HOH HOH . I 5 HOH B 17 617 83 HOH HOH . I 5 HOH B 18 618 111 HOH HOH . I 5 HOH B 19 619 76 HOH HOH . I 5 HOH B 20 620 32 HOH HOH . I 5 HOH B 21 621 129 HOH HOH . I 5 HOH B 22 622 53 HOH HOH . I 5 HOH B 23 623 7 HOH HOH . I 5 HOH B 24 624 24 HOH HOH . I 5 HOH B 25 625 25 HOH HOH . I 5 HOH B 26 626 150 HOH HOH . I 5 HOH B 27 627 98 HOH HOH . I 5 HOH B 28 628 44 HOH HOH . I 5 HOH B 29 629 114 HOH HOH . I 5 HOH B 30 630 82 HOH HOH . I 5 HOH B 31 631 127 HOH HOH . I 5 HOH B 32 632 194 HOH HOH . I 5 HOH B 33 633 167 HOH HOH . I 5 HOH B 34 634 158 HOH HOH . I 5 HOH B 35 635 202 HOH HOH . I 5 HOH B 36 636 164 HOH HOH . I 5 HOH B 37 637 73 HOH HOH . I 5 HOH B 38 638 104 HOH HOH . I 5 HOH B 39 639 171 HOH HOH . I 5 HOH B 40 640 79 HOH HOH . I 5 HOH B 41 641 23 HOH HOH . I 5 HOH B 42 642 100 HOH HOH . I 5 HOH B 43 643 18 HOH HOH . I 5 HOH B 44 644 2 HOH HOH . I 5 HOH B 45 645 20 HOH HOH . I 5 HOH B 46 646 160 HOH HOH . I 5 HOH B 47 647 42 HOH HOH . I 5 HOH B 48 648 31 HOH HOH . I 5 HOH B 49 649 95 HOH HOH . I 5 HOH B 50 650 57 HOH HOH . I 5 HOH B 51 651 183 HOH HOH . I 5 HOH B 52 652 1 HOH HOH . I 5 HOH B 53 653 80 HOH HOH . I 5 HOH B 54 654 103 HOH HOH . I 5 HOH B 55 655 142 HOH HOH . I 5 HOH B 56 656 15 HOH HOH . I 5 HOH B 57 657 141 HOH HOH . I 5 HOH B 58 658 190 HOH HOH . I 5 HOH B 59 659 35 HOH HOH . I 5 HOH B 60 660 170 HOH HOH . I 5 HOH B 61 661 116 HOH HOH . I 5 HOH B 62 662 124 HOH HOH . I 5 HOH B 63 663 139 HOH HOH . I 5 HOH B 64 664 147 HOH HOH . I 5 HOH B 65 665 10 HOH HOH . I 5 HOH B 66 666 93 HOH HOH . I 5 HOH B 67 667 78 HOH HOH . I 5 HOH B 68 668 119 HOH HOH . I 5 HOH B 69 669 72 HOH HOH . I 5 HOH B 70 670 12 HOH HOH . I 5 HOH B 71 671 84 HOH HOH . I 5 HOH B 72 672 40 HOH HOH . I 5 HOH B 73 673 123 HOH HOH . I 5 HOH B 74 674 69 HOH HOH . I 5 HOH B 75 675 81 HOH HOH . I 5 HOH B 76 676 46 HOH HOH . I 5 HOH B 77 677 137 HOH HOH . I 5 HOH B 78 678 145 HOH HOH . I 5 HOH B 79 679 71 HOH HOH . I 5 HOH B 80 680 50 HOH HOH . I 5 HOH B 81 681 179 HOH HOH . I 5 HOH B 82 682 58 HOH HOH . I 5 HOH B 83 683 51 HOH HOH . I 5 HOH B 84 684 27 HOH HOH . I 5 HOH B 85 685 140 HOH HOH . I 5 HOH B 86 686 63 HOH HOH . I 5 HOH B 87 687 67 HOH HOH . I 5 HOH B 88 688 149 HOH HOH . I 5 HOH B 89 689 66 HOH HOH . I 5 HOH B 90 690 155 HOH HOH . I 5 HOH B 91 691 148 HOH HOH . I 5 HOH B 92 692 34 HOH HOH . I 5 HOH B 93 693 77 HOH HOH . I 5 HOH B 94 694 96 HOH HOH . I 5 HOH B 95 695 159 HOH HOH . I 5 HOH B 96 696 169 HOH HOH . I 5 HOH B 97 697 201 HOH HOH . I 5 HOH B 98 698 101 HOH HOH . I 5 HOH B 99 699 113 HOH HOH . I 5 HOH B 100 700 38 HOH HOH . I 5 HOH B 101 701 157 HOH HOH . I 5 HOH B 102 702 192 HOH HOH . I 5 HOH B 103 703 120 HOH HOH . I 5 HOH B 104 704 122 HOH HOH . I 5 HOH B 105 705 88 HOH HOH . I 5 HOH B 106 706 200 HOH HOH . I 5 HOH B 107 707 197 HOH HOH . I 5 HOH B 108 708 143 HOH HOH . I 5 HOH B 109 709 176 HOH HOH . I 5 HOH B 110 710 106 HOH HOH . I 5 HOH B 111 711 138 HOH HOH . I 5 HOH B 112 712 75 HOH HOH . I 5 HOH B 113 713 107 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 N N UYM . . . G 4 -14.218 33.255 19.45 1 70.99 ? N UYM 503 B 1 HETATM 2 C C UYM . . . G 4 -19.84 31.89 20.696 1 73.95 ? C UYM 503 B 1 HETATM 3 O O UYM . . . G 4 -20.284 33.047 20.673 1 61.77 ? O UYM 503 B 1 HETATM 4 C C1 UYM . . . G 4 -18.338 31.671 20.72 1 77.6 ? C1 UYM 503 B 1 HETATM 5 C C10 UYM . . . G 4 -12.738 31.209 19.355 1 78.8 ? C10 UYM 503 B 1 HETATM 6 C C11 UYM . . . G 4 -20.203 29.415 20.679 1 79.7 ? C11 UYM 503 B 1 HETATM 7 C C12 UYM . . . G 4 -20.535 28.734 19.323 1 80.99 ? C12 UYM 503 B 1 HETATM 8 C C15 UYM . . . G 4 -18.735 29.217 21.007 1 79.81 ? C15 UYM 503 B 1 HETATM 9 C C2 UYM . . . G 4 -17.717 32.074 19.355 1 72.54 ? C2 UYM 503 B 1 HETATM 10 C C3 UYM . . . G 4 -16.226 32.257 19.373 1 76.41 ? C3 UYM 503 B 1 HETATM 11 C C34 UYM . . . G 4 -20.06 29.444 18.083 1 74.34 ? C34 UYM 503 B 1 HETATM 12 C C35 UYM . . . G 4 -20.696 30.497 17.489 1 69.14 ? C35 UYM 503 B 1 HETATM 13 C C37 UYM . . . G 4 -18.914 30.099 16.206 1 79.01 ? C37 UYM 503 B 1 HETATM 14 C C38 UYM . . . G 4 -18.9 29.167 17.27 1 77.8 ? C38 UYM 503 B 1 HETATM 15 C C39 UYM . . . G 4 -17.864 28.225 17.338 1 77.07 ? C39 UYM 503 B 1 HETATM 16 C C4 UYM . . . G 4 -15.576 33.46 19.442 1 68.04 ? C4 UYM 503 B 1 HETATM 17 C C40 UYM . . . G 4 -16.892 28.238 16.363 1 72.57 ? C40 UYM 503 B 1 HETATM 18 C C41 UYM . . . G 4 -16.926 29.175 15.324 1 77.37 ? C41 UYM 503 B 1 HETATM 19 C C42 UYM . . . G 4 -17.925 30.118 15.221 1 72.63 ? C42 UYM 503 B 1 HETATM 20 C C5 UYM . . . G 4 -13.953 31.906 19.375 1 79.27 ? C5 UYM 503 B 1 HETATM 21 C C6 UYM . . . G 4 -15.198 31.234 19.32 1 78.53 ? C6 UYM 503 B 1 HETATM 22 C C7 UYM . . . G 4 -15.206 29.828 19.249 1 74.93 ? C7 UYM 503 B 1 HETATM 23 C C8 UYM . . . G 4 -14.004 29.144 19.23 1 71.14 ? C8 UYM 503 B 1 HETATM 24 C C9 UYM . . . G 4 -12.79 29.829 19.288 1 76.12 ? C9 UYM 503 B 1 HETATM 25 N N1 UYM . . . G 4 -17.963 30.305 21.087 1 79.68 ? N1 UYM 503 B 1 HETATM 26 N N2 UYM . . . G 4 -20.627 30.816 20.695 1 77.8 ? N2 UYM 503 B 1 HETATM 27 N N36 UYM . . . G 4 -20.025 30.886 16.364 1 72.83 ? N36 UYM 503 B 1 HETATM 28 O O1 UYM . . . G 4 -18.313 28.059 21.177 1 61.23 ? O1 UYM 503 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #