data_1YEK # _model_server_result.job_id Ysi2sExwYGNCOaNvePMAtA _model_server_result.datetime_utc '2025-02-26 19:24:49' _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 1yek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":551}' # _entry.id 1YEK # _exptl.entry_id 1YEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 139.109 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description P-NITROPHENOL _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 1YEK _cell.length_a 78.73 _cell.length_b 78.73 _cell.length_c 159.03 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YEK _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 PISA dimeric 2 author_and_software_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,H,I,J,K,L 1 1 A,C,D,E,F,G,H,I,K 2 1 B,J,L 2 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_665 x-y+1,-y+1,-z+2/3 1 0 0 0 -1 0 0 0 -1 39.365 68.18218 106.02 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id J _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 23 L CYS 23 1_555 A SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf2 A SG CYS 139 L CYS 134 1_555 A SG CYS 199 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 B SG CYS 150 H CYS 140 1_555 B SG CYS 205 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 A NE2 HIS 54 L HIS 49 1_555 G ZN ZN . L ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc2 A OD2 ASP 65 L ASP 60 4_456 D ZN ZN . L ZN 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc3 A ND1 HIS 98 L HIS 93 1_555 H ZN ZN . L ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc4 A OD2 ASP 156 L ASP 151 1_555 C ZN ZN . L ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc5 A ND1 HIS 194 L HIS 189 1_555 C ZN ZN . L ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 E ZN ZN . L ZN 601 1_555 K O HOH . L HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc7 E ZN ZN . L ZN 601 1_555 K O HOH . L HOH 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.692 ? metalc ? metalc8 E ZN ZN . L ZN 601 1_555 K O HOH . L HOH 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? metalc ? metalc9 F ZN ZN . L ZN 602 1_555 K O HOH . L HOH 663 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc10 F ZN ZN . L ZN 602 1_555 K O HOH . L HOH 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? metalc ? metalc11 F ZN ZN . L ZN 602 1_555 K O HOH . L HOH 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc12 G ZN ZN . L ZN 603 1_555 K O HOH . L HOH 677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? metalc ? metalc13 G ZN ZN . L ZN 603 1_555 B OD1 ASP 107 H ASP 100 1_555 ? ? ? C ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc14 G ZN ZN . L ZN 603 1_555 L O HOH . H HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? metalc ? metalc15 H ZN ZN . L ZN 604 1_555 K O HOH . L HOH 643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc16 H ZN ZN . L ZN 604 1_555 K O HOH . L HOH 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.646 ? metalc ? metalc17 H ZN ZN . L ZN 604 1_555 B OD1 ASP 183 H ASP 181 5_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc18 C ZN ZN . L ZN 605 1_555 K O HOH . L HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? metalc ? metalc19 C ZN ZN . L ZN 605 1_555 K O HOH . L HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.715 ? metalc ? metalc20 I ZN ZN . L ZN 606 1_555 K O HOH . L HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc21 I ZN ZN . L ZN 606 1_555 K O HOH . L HOH 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc22 I ZN ZN . L ZN 606 1_555 K O HOH . L HOH 679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.647 ? metalc ? metalc23 I ZN ZN . L ZN 606 1_555 K O HOH . L HOH 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.586 ? metalc ? metalc24 D ZN ZN . L ZN 607 1_555 K O HOH . L HOH 655 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc25 D ZN ZN . L ZN 607 1_555 K O HOH . L HOH 656 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc26 D ZN ZN . L ZN 607 1_555 K O HOH . L HOH 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? # _chem_comp.formula 'C6 H5 N O3' _chem_comp.formula_weight 139.109 _chem_comp.id NPO _chem_comp.mon_nstd_flag . _chem_comp.name P-NITROPHENOL _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 C1 C2 NPO doub 237 n y C1 C6 NPO sing 238 n y C1 N1 NPO sing 239 n n C2 C3 NPO sing 240 n y C2 H2 NPO sing 241 n n C3 C4 NPO doub 242 n y C3 H3 NPO sing 243 n n C4 C5 NPO sing 244 n y C4 OH NPO sing 245 n n C5 C6 NPO doub 246 n y C5 H5 NPO sing 247 n n C6 H6 NPO sing 248 n n OH HO NPO sing 249 n n N1 O2 NPO sing 250 n n N1 O3 NPO doub 251 n n # _atom_sites.entry_id 1YEK _atom_sites.fract_transf_matrix[1][1] 0.012702 _atom_sites.fract_transf_matrix[1][2] 0.007333 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014666 _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] 0.006288 _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 3 ZN L 1 605 5 ZN ZN . D 3 ZN L 1 607 7 ZN ZN . E 3 ZN L 1 601 1 ZN ZN . F 3 ZN L 1 602 2 ZN ZN . G 3 ZN L 1 603 3 ZN ZN . H 3 ZN L 1 604 4 ZN ZN . I 3 ZN L 1 606 6 ZN ZN . J 4 NPO H 1 551 551 NPO PNP . K 5 HOH L 1 608 1 HOH HOH . K 5 HOH L 2 609 2 HOH HOH . K 5 HOH L 3 610 4 HOH HOH . K 5 HOH L 4 611 5 HOH HOH . K 5 HOH L 5 612 7 HOH HOH . K 5 HOH L 6 613 10 HOH HOH . K 5 HOH L 7 614 16 HOH HOH . K 5 HOH L 8 615 17 HOH HOH . K 5 HOH L 9 616 18 HOH HOH . K 5 HOH L 10 617 20 HOH HOH . K 5 HOH L 11 618 21 HOH HOH . K 5 HOH L 12 619 23 HOH HOH . K 5 HOH L 13 620 24 HOH HOH . K 5 HOH L 14 621 26 HOH HOH . K 5 HOH L 15 622 28 HOH HOH . K 5 HOH L 16 623 30 HOH HOH . K 5 HOH L 17 624 31 HOH HOH . K 5 HOH L 18 625 34 HOH HOH . K 5 HOH L 19 626 36 HOH HOH . K 5 HOH L 20 627 41 HOH HOH . K 5 HOH L 21 628 43 HOH HOH . K 5 HOH L 22 629 44 HOH HOH . K 5 HOH L 23 630 45 HOH HOH . K 5 HOH L 24 631 46 HOH HOH . K 5 HOH L 25 632 47 HOH HOH . K 5 HOH L 26 633 48 HOH HOH . K 5 HOH L 27 634 50 HOH HOH . K 5 HOH L 28 635 51 HOH HOH . K 5 HOH L 29 636 52 HOH HOH . K 5 HOH L 30 637 53 HOH HOH . K 5 HOH L 31 638 54 HOH HOH . K 5 HOH L 32 639 55 HOH HOH . K 5 HOH L 33 640 57 HOH HOH . K 5 HOH L 34 641 61 HOH HOH . K 5 HOH L 35 642 62 HOH HOH . K 5 HOH L 36 643 63 HOH HOH . K 5 HOH L 37 644 66 HOH HOH . K 5 HOH L 38 645 69 HOH HOH . K 5 HOH L 39 646 70 HOH HOH . K 5 HOH L 40 647 71 HOH HOH . K 5 HOH L 41 648 73 HOH HOH . K 5 HOH L 42 649 77 HOH HOH . K 5 HOH L 43 650 78 HOH HOH . K 5 HOH L 44 651 79 HOH HOH . K 5 HOH L 45 652 82 HOH HOH . K 5 HOH L 46 653 83 HOH HOH . K 5 HOH L 47 654 87 HOH HOH . K 5 HOH L 48 655 89 HOH HOH . K 5 HOH L 49 656 91 HOH HOH . K 5 HOH L 50 657 94 HOH HOH . K 5 HOH L 51 658 100 HOH HOH . K 5 HOH L 52 659 101 HOH HOH . K 5 HOH L 53 660 104 HOH HOH . K 5 HOH L 54 661 107 HOH HOH . K 5 HOH L 55 662 110 HOH HOH . K 5 HOH L 56 663 115 HOH HOH . K 5 HOH L 57 664 116 HOH HOH . K 5 HOH L 58 665 120 HOH HOH . K 5 HOH L 59 666 125 HOH HOH . K 5 HOH L 60 667 126 HOH HOH . K 5 HOH L 61 668 127 HOH HOH . K 5 HOH L 62 669 128 HOH HOH . K 5 HOH L 63 670 129 HOH HOH . K 5 HOH L 64 671 131 HOH HOH . K 5 HOH L 65 672 135 HOH HOH . K 5 HOH L 66 673 141 HOH HOH . K 5 HOH L 67 674 1 HOH ZN . K 5 HOH L 68 675 1 HOH ZN . K 5 HOH L 69 676 2 HOH ZN . K 5 HOH L 70 677 3 HOH ZN . K 5 HOH L 71 678 4 HOH ZN . K 5 HOH L 72 679 6 HOH ZN . K 5 HOH L 73 680 6 HOH ZN . L 5 HOH H 1 552 3 HOH HOH . L 5 HOH H 2 553 6 HOH HOH . L 5 HOH H 3 554 8 HOH HOH . L 5 HOH H 4 555 9 HOH HOH . L 5 HOH H 5 556 11 HOH HOH . L 5 HOH H 6 557 12 HOH HOH . L 5 HOH H 7 558 13 HOH HOH . L 5 HOH H 8 559 14 HOH HOH . L 5 HOH H 9 560 15 HOH HOH . L 5 HOH H 10 561 19 HOH HOH . L 5 HOH H 11 562 22 HOH HOH . L 5 HOH H 12 563 25 HOH HOH . L 5 HOH H 13 564 27 HOH HOH . L 5 HOH H 14 565 29 HOH HOH . L 5 HOH H 15 566 32 HOH HOH . L 5 HOH H 16 567 33 HOH HOH . L 5 HOH H 17 568 35 HOH HOH . L 5 HOH H 18 569 37 HOH HOH . L 5 HOH H 19 570 38 HOH HOH . L 5 HOH H 20 571 39 HOH HOH . L 5 HOH H 21 572 40 HOH HOH . L 5 HOH H 22 573 42 HOH HOH . L 5 HOH H 23 574 49 HOH HOH . L 5 HOH H 24 575 56 HOH HOH . L 5 HOH H 25 576 58 HOH HOH . L 5 HOH H 26 577 59 HOH HOH . L 5 HOH H 27 578 64 HOH HOH . L 5 HOH H 28 579 65 HOH HOH . L 5 HOH H 29 580 68 HOH HOH . L 5 HOH H 30 581 74 HOH HOH . L 5 HOH H 31 582 75 HOH HOH . L 5 HOH H 32 583 76 HOH HOH . L 5 HOH H 33 584 80 HOH HOH . L 5 HOH H 34 585 84 HOH HOH . L 5 HOH H 35 586 86 HOH HOH . L 5 HOH H 36 587 92 HOH HOH . L 5 HOH H 37 588 93 HOH HOH . L 5 HOH H 38 589 95 HOH HOH . L 5 HOH H 39 590 96 HOH HOH . L 5 HOH H 40 591 97 HOH HOH . L 5 HOH H 41 592 99 HOH HOH . L 5 HOH H 42 593 102 HOH HOH . L 5 HOH H 43 594 103 HOH HOH . L 5 HOH H 44 595 106 HOH HOH . L 5 HOH H 45 596 108 HOH HOH . L 5 HOH H 46 597 114 HOH HOH . L 5 HOH H 47 598 117 HOH HOH . L 5 HOH H 48 599 119 HOH HOH . L 5 HOH H 49 600 122 HOH HOH . L 5 HOH H 50 601 124 HOH HOH . L 5 HOH H 51 602 132 HOH HOH . L 5 HOH H 52 603 133 HOH HOH . L 5 HOH H 53 604 134 HOH HOH . L 5 HOH H 54 605 136 HOH HOH . L 5 HOH H 55 606 137 HOH HOH . L 5 HOH H 56 607 138 HOH HOH . L 5 HOH H 57 608 139 HOH HOH . L 5 HOH H 58 609 140 HOH HOH . L 5 HOH H 59 610 142 HOH HOH . L 5 HOH H 60 611 3 HOH ZN . # 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 C1 NPO . . . J 4 8.91 39.648 61.906 1 23.43 ? C1 NPO 551 H 1 HETATM 2 C C2 NPO . . . J 4 10.07 40.068 61.323 1 21.36 ? C2 NPO 551 H 1 HETATM 3 C C3 NPO . . . J 4 11.137 39.196 61.264 1 23.94 ? C3 NPO 551 H 1 HETATM 4 C C4 NPO . . . J 4 11.038 37.914 61.785 1 22.64 ? C4 NPO 551 H 1 HETATM 5 C C5 NPO . . . J 4 9.866 37.477 62.37 1 22.96 ? C5 NPO 551 H 1 HETATM 6 C C6 NPO . . . J 4 8.799 38.352 62.428 1 23.37 ? C6 NPO 551 H 1 HETATM 7 O OH NPO . . . J 4 12.127 37.088 61.72 1 27.59 ? OH NPO 551 H 1 HETATM 8 N N1 NPO . . . J 4 7.794 40.574 62.035 1 25.25 ? N1 NPO 551 H 1 HETATM 9 O O2 NPO . . . J 4 7.893 41.764 61.696 1 27.39 ? O2 NPO 551 H 1 HETATM 10 O O3 NPO . . . J 4 6.743 40.151 62.503 1 28.58 ? O3 NPO 551 H 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #