data_5YVC # _model_server_result.job_id 5-xrSp1n2wxlDAM6aMmlYQ _model_server_result.datetime_utc '2024-12-02 07:54:35' _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 5yvc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5YVC # _exptl.entry_id 5YVC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.347 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid' _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 5YVC _cell.length_a 66.332 _cell.length_b 77.831 _cell.length_c 84.155 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVC _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 2 _struct_asym.id B _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 MET 246 A MET 396 1_555 A N CAS 247 A CAS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C CAS 247 A CAS 397 1_555 A N LEU 248 A LEU 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C18 H18 N2 O3' _chem_comp.formula_weight 310.347 _chem_comp.id SU6 _chem_comp.mon_nstd_flag . _chem_comp.name '3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SU6668 # 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 O2 C1 SU6 doub 347 n n O1 C1 SU6 sing 348 n n C1 C2 SU6 sing 349 n n C2 C3 SU6 sing 350 n n C3 C4 SU6 sing 351 n n C4 C7 SU6 sing 352 n y C4 C5 SU6 doub 353 n y C8 C7 SU6 sing 354 n n C6 C5 SU6 sing 355 n n C7 C9 SU6 doub 356 n y C5 N1 SU6 sing 357 n y C9 N1 SU6 sing 358 n y C9 C10 SU6 sing 359 n n C10 C11 SU6 doub 360 z n O3 C12 SU6 doub 361 n n C11 C12 SU6 sing 362 n n C11 C13 SU6 sing 363 n n C12 N2 SU6 sing 364 n n C13 C18 SU6 doub 365 n y C13 C14 SU6 sing 366 n y C18 C17 SU6 sing 367 n y N2 C14 SU6 sing 368 n n C14 C15 SU6 doub 369 n y C17 C16 SU6 doub 370 n y C15 C16 SU6 sing 371 n y N1 H1 SU6 sing 372 n n O1 H2 SU6 sing 373 n n C2 H3 SU6 sing 374 n n N2 H4 SU6 sing 375 n n C3 H5 SU6 sing 376 n n C6 H6 SU6 sing 377 n n C6 H7 SU6 sing 378 n n C6 H8 SU6 sing 379 n n C8 H9 SU6 sing 380 n n C8 H10 SU6 sing 381 n n C8 H11 SU6 sing 382 n n C10 H12 SU6 sing 383 n n C15 H15 SU6 sing 384 n n C16 H16 SU6 sing 385 n n C17 H17 SU6 sing 386 n n C18 H18 SU6 sing 387 n n C2 H19 SU6 sing 388 n n C3 H20 SU6 sing 389 n n # _atom_sites.entry_id 5YVC _atom_sites.fract_transf_matrix[1][1] 0.015076 _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] 0.012848 _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] 0.011883 _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 SU6 A 1 501 501 SU6 C12 . C 3 GOL A 1 502 601 GOL GOL . D 3 GOL A 1 503 602 GOL GOL . E 3 GOL A 1 504 603 GOL GOL . F 4 PGE A 1 505 604 PGE PGE . G 5 CL A 1 506 701 CL CL . H 6 HOH A 1 601 191 HOH HOH . H 6 HOH A 2 602 192 HOH HOH . H 6 HOH A 3 603 67 HOH HOH . H 6 HOH A 4 604 125 HOH HOH . H 6 HOH A 5 605 142 HOH HOH . H 6 HOH A 6 606 37 HOH HOH . H 6 HOH A 7 607 108 HOH HOH . H 6 HOH A 8 608 143 HOH HOH . H 6 HOH A 9 609 150 HOH HOH . H 6 HOH A 10 610 93 HOH HOH . H 6 HOH A 11 611 48 HOH HOH . H 6 HOH A 12 612 24 HOH HOH . H 6 HOH A 13 613 199 HOH HOH . H 6 HOH A 14 614 45 HOH HOH . H 6 HOH A 15 615 12 HOH HOH . H 6 HOH A 16 616 73 HOH HOH . H 6 HOH A 17 617 182 HOH HOH . H 6 HOH A 18 618 101 HOH HOH . H 6 HOH A 19 619 71 HOH HOH . H 6 HOH A 20 620 4 HOH HOH . H 6 HOH A 21 621 39 HOH HOH . H 6 HOH A 22 622 144 HOH HOH . H 6 HOH A 23 623 88 HOH HOH . H 6 HOH A 24 624 149 HOH HOH . H 6 HOH A 25 625 66 HOH HOH . H 6 HOH A 26 626 6 HOH HOH . H 6 HOH A 27 627 64 HOH HOH . H 6 HOH A 28 628 198 HOH HOH . H 6 HOH A 29 629 19 HOH HOH . H 6 HOH A 30 630 54 HOH HOH . H 6 HOH A 31 631 102 HOH HOH . H 6 HOH A 32 632 104 HOH HOH . H 6 HOH A 33 633 50 HOH HOH . H 6 HOH A 34 634 62 HOH HOH . H 6 HOH A 35 635 29 HOH HOH . H 6 HOH A 36 636 167 HOH HOH . H 6 HOH A 37 637 151 HOH HOH . H 6 HOH A 38 638 3 HOH HOH . H 6 HOH A 39 639 42 HOH HOH . H 6 HOH A 40 640 7 HOH HOH . H 6 HOH A 41 641 89 HOH HOH . H 6 HOH A 42 642 2 HOH HOH . H 6 HOH A 43 643 94 HOH HOH . H 6 HOH A 44 644 69 HOH HOH . H 6 HOH A 45 645 170 HOH HOH . H 6 HOH A 46 646 76 HOH HOH . H 6 HOH A 47 647 59 HOH HOH . H 6 HOH A 48 648 56 HOH HOH . H 6 HOH A 49 649 79 HOH HOH . H 6 HOH A 50 650 90 HOH HOH . H 6 HOH A 51 651 70 HOH HOH . H 6 HOH A 52 652 5 HOH HOH . H 6 HOH A 53 653 28 HOH HOH . H 6 HOH A 54 654 111 HOH HOH . H 6 HOH A 55 655 153 HOH HOH . H 6 HOH A 56 656 115 HOH HOH . H 6 HOH A 57 657 10 HOH HOH . H 6 HOH A 58 658 169 HOH HOH . H 6 HOH A 59 659 181 HOH HOH . H 6 HOH A 60 660 27 HOH HOH . H 6 HOH A 61 661 47 HOH HOH . H 6 HOH A 62 662 99 HOH HOH . H 6 HOH A 63 663 74 HOH HOH . H 6 HOH A 64 664 171 HOH HOH . H 6 HOH A 65 665 38 HOH HOH . H 6 HOH A 66 666 49 HOH HOH . H 6 HOH A 67 667 163 HOH HOH . H 6 HOH A 68 668 175 HOH HOH . H 6 HOH A 69 669 180 HOH HOH . H 6 HOH A 70 670 9 HOH HOH . H 6 HOH A 71 671 121 HOH HOH . H 6 HOH A 72 672 154 HOH HOH . H 6 HOH A 73 673 166 HOH HOH . H 6 HOH A 74 674 157 HOH HOH . H 6 HOH A 75 675 17 HOH HOH . H 6 HOH A 76 676 32 HOH HOH . H 6 HOH A 77 677 200 HOH HOH . H 6 HOH A 78 678 1 HOH HOH . H 6 HOH A 79 679 14 HOH HOH . H 6 HOH A 80 680 100 HOH HOH . H 6 HOH A 81 681 82 HOH HOH . H 6 HOH A 82 682 145 HOH HOH . H 6 HOH A 83 683 30 HOH HOH . H 6 HOH A 84 684 156 HOH HOH . H 6 HOH A 85 685 96 HOH HOH . H 6 HOH A 86 686 43 HOH HOH . H 6 HOH A 87 687 87 HOH HOH . H 6 HOH A 88 688 63 HOH HOH . H 6 HOH A 89 689 164 HOH HOH . H 6 HOH A 90 690 196 HOH HOH . H 6 HOH A 91 691 126 HOH HOH . H 6 HOH A 92 692 65 HOH HOH . H 6 HOH A 93 693 18 HOH HOH . H 6 HOH A 94 694 13 HOH HOH . H 6 HOH A 95 695 68 HOH HOH . H 6 HOH A 96 696 139 HOH HOH . H 6 HOH A 97 697 51 HOH HOH . H 6 HOH A 98 698 158 HOH HOH . H 6 HOH A 99 699 36 HOH HOH . H 6 HOH A 100 700 60 HOH HOH . H 6 HOH A 101 701 114 HOH HOH . H 6 HOH A 102 702 58 HOH HOH . H 6 HOH A 103 703 148 HOH HOH . H 6 HOH A 104 704 11 HOH HOH . H 6 HOH A 105 705 147 HOH HOH . H 6 HOH A 106 706 20 HOH HOH . H 6 HOH A 107 707 95 HOH HOH . H 6 HOH A 108 708 22 HOH HOH . H 6 HOH A 109 709 46 HOH HOH . H 6 HOH A 110 710 91 HOH HOH . H 6 HOH A 111 711 92 HOH HOH . H 6 HOH A 112 712 25 HOH HOH . H 6 HOH A 113 713 110 HOH HOH . H 6 HOH A 114 714 86 HOH HOH . H 6 HOH A 115 715 77 HOH HOH . H 6 HOH A 116 716 55 HOH HOH . H 6 HOH A 117 717 186 HOH HOH . H 6 HOH A 118 718 26 HOH HOH . H 6 HOH A 119 719 31 HOH HOH . H 6 HOH A 120 720 53 HOH HOH . H 6 HOH A 121 721 98 HOH HOH . H 6 HOH A 122 722 8 HOH HOH . H 6 HOH A 123 723 123 HOH HOH . H 6 HOH A 124 724 33 HOH HOH . H 6 HOH A 125 725 132 HOH HOH . H 6 HOH A 126 726 78 HOH HOH . H 6 HOH A 127 727 122 HOH HOH . H 6 HOH A 128 728 160 HOH HOH . H 6 HOH A 129 729 124 HOH HOH . H 6 HOH A 130 730 138 HOH HOH . H 6 HOH A 131 731 41 HOH HOH . H 6 HOH A 132 732 109 HOH HOH . H 6 HOH A 133 733 129 HOH HOH . H 6 HOH A 134 734 113 HOH HOH . H 6 HOH A 135 735 116 HOH HOH . H 6 HOH A 136 736 23 HOH HOH . H 6 HOH A 137 737 134 HOH HOH . H 6 HOH A 138 738 80 HOH HOH . H 6 HOH A 139 739 140 HOH HOH . H 6 HOH A 140 740 44 HOH HOH . H 6 HOH A 141 741 117 HOH HOH . H 6 HOH A 142 742 81 HOH HOH . H 6 HOH A 143 743 190 HOH HOH . H 6 HOH A 144 744 15 HOH HOH . H 6 HOH A 145 745 146 HOH HOH . H 6 HOH A 146 746 202 HOH HOH . H 6 HOH A 147 747 118 HOH HOH . H 6 HOH A 148 748 130 HOH HOH . H 6 HOH A 149 749 189 HOH HOH . H 6 HOH A 150 750 120 HOH HOH . H 6 HOH A 151 751 131 HOH HOH . H 6 HOH A 152 752 34 HOH HOH . H 6 HOH A 153 753 197 HOH HOH . H 6 HOH A 154 754 105 HOH HOH . H 6 HOH A 155 755 16 HOH HOH . H 6 HOH A 156 756 176 HOH HOH . H 6 HOH A 157 757 137 HOH HOH . H 6 HOH A 158 758 152 HOH HOH . H 6 HOH A 159 759 83 HOH HOH . H 6 HOH A 160 760 141 HOH HOH . H 6 HOH A 161 761 195 HOH HOH . H 6 HOH A 162 762 172 HOH HOH . H 6 HOH A 163 763 61 HOH HOH . H 6 HOH A 164 764 173 HOH HOH . H 6 HOH A 165 765 187 HOH HOH . H 6 HOH A 166 766 119 HOH HOH . H 6 HOH A 167 767 188 HOH HOH . H 6 HOH A 168 768 177 HOH HOH . H 6 HOH A 169 769 183 HOH HOH . H 6 HOH A 170 770 185 HOH HOH . H 6 HOH A 171 771 193 HOH HOH . H 6 HOH A 172 772 85 HOH HOH . H 6 HOH A 173 773 162 HOH HOH . H 6 HOH A 174 774 194 HOH HOH . H 6 HOH A 175 775 184 HOH HOH . H 6 HOH A 176 776 52 HOH HOH . H 6 HOH A 177 777 40 HOH HOH . H 6 HOH A 178 778 84 HOH HOH . H 6 HOH A 179 779 112 HOH HOH . H 6 HOH A 180 780 72 HOH HOH . H 6 HOH A 181 781 97 HOH HOH . H 6 HOH A 182 782 168 HOH HOH . H 6 HOH A 183 783 35 HOH HOH . H 6 HOH A 184 784 103 HOH HOH . H 6 HOH A 185 785 128 HOH HOH . H 6 HOH A 186 786 159 HOH HOH . H 6 HOH A 187 787 106 HOH HOH . H 6 HOH A 188 788 21 HOH HOH . H 6 HOH A 189 789 107 HOH HOH . H 6 HOH A 190 790 127 HOH HOH . H 6 HOH A 191 791 57 HOH HOH . H 6 HOH A 192 792 75 HOH HOH . H 6 HOH A 193 793 165 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 C1 SU6 . . . B 2 -2.219 -11.183 26.759 1 69.92 ? C1 SU6 501 A 1 HETATM 2 N N1 SU6 . . . B 2 -0.206 -5.243 26.274 1 49.88 ? N1 SU6 501 A 1 HETATM 3 O O1 SU6 . . . B 2 -3.252 -11.831 27.049 1 71.83 ? O1 SU6 501 A 1 HETATM 4 C C2 SU6 . . . B 2 -2.179 -9.624 26.995 1 66.1 ? C2 SU6 501 A 1 HETATM 5 N N2 SU6 . . . B 2 0.097 -0.993 25.149 1 74.89 ? N2 SU6 501 A 1 HETATM 6 O O2 SU6 . . . B 2 -1.178 -11.684 26.257 1 66.83 -1 O2 SU6 501 A 1 HETATM 7 C C3 SU6 . . . B 2 -1.015 -8.897 26.308 1 53.26 ? C3 SU6 501 A 1 HETATM 8 O O3 SU6 . . . B 2 0.598 -3.05 26.097 1 59.64 ? O3 SU6 501 A 1 HETATM 9 C C4 SU6 . . . B 2 -1.01 -7.382 26.202 1 55.82 ? C4 SU6 501 A 1 HETATM 10 C C5 SU6 . . . B 2 0.099 -6.588 26.535 1 56.07 ? C5 SU6 501 A 1 HETATM 11 C C6 SU6 . . . B 2 1.433 -6.96 27.083 1 69.34 ? C6 SU6 501 A 1 HETATM 12 C C7 SU6 . . . B 2 -2.009 -6.466 25.695 1 46.85 ? C7 SU6 501 A 1 HETATM 13 C C8 SU6 . . . B 2 -3.358 -6.801 25.197 1 48.06 ? C8 SU6 501 A 1 HETATM 14 C C9 SU6 . . . B 2 -1.506 -5.147 25.761 1 49.27 ? C9 SU6 501 A 1 HETATM 15 C C10 SU6 . . . B 2 -2.155 -3.88 25.356 1 53.75 ? C10 SU6 501 A 1 HETATM 16 C C11 SU6 . . . B 2 -1.594 -2.668 25.118 1 59.95 ? C11 SU6 501 A 1 HETATM 17 C C12 SU6 . . . B 2 -0.246 -2.327 25.509 1 68.33 ? C12 SU6 501 A 1 HETATM 18 C C13 SU6 . . . B 2 -2.085 -1.437 24.47 1 51.85 ? C13 SU6 501 A 1 HETATM 19 C C14 SU6 . . . B 2 -1.059 -0.453 24.506 1 61.68 ? C14 SU6 501 A 1 HETATM 20 C C15 SU6 . . . B 2 -1.238 0.824 23.964 1 57.14 ? C15 SU6 501 A 1 HETATM 21 C C16 SU6 . . . B 2 -2.488 1.098 23.38 1 58.04 ? C16 SU6 501 A 1 HETATM 22 C C17 SU6 . . . B 2 -3.497 0.157 23.345 1 46.95 ? C17 SU6 501 A 1 HETATM 23 C C18 SU6 . . . B 2 -3.292 -1.12 23.89 1 51.15 ? C18 SU6 501 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #