data_6PTQ # _model_server_result.job_id k_wn9jcZAUgn3q_f7XiUjg _model_server_result.datetime_utc '2024-11-13 08:53:07' _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 6ptq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6PTQ # _exptl.entry_id 6PTQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 584.662 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.63 _cell.angle_gamma 90 _cell.entry_id 6PTQ _cell.length_a 83.69 _cell.length_b 83.4 _cell.length_c 86.87 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PTQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 ? 2 C N N ? 2 E 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 covale ? covale1 A SG CYS 5 A CYS 13 1_555 C CBA EL5 . A EL5 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? covale ? covale2 B SG CYS 5 B CYS 13 1_555 E CBA EL5 . B EL5 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? # _chem_comp.formula 'C33 H36 N4 O6' _chem_comp.formula_weight 584.662 _chem_comp.id EL5 _chem_comp.mon_nstd_flag . _chem_comp.name '3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'biliverdin, bound form at Pfr state' # 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 OD C4D EL5 doub 100 n n ND C4D EL5 sing 101 n n ND C1D EL5 sing 102 n n CMA C2A EL5 sing 103 n n CBA CAA EL5 sing 104 n n C4D C3D EL5 sing 105 n n C2A C1A EL5 sing 106 n n C2A C3A EL5 sing 107 n n OA C1A EL5 doub 108 n n CBD CAD EL5 doub 109 n n CAA C3A EL5 doub 110 e n C1A NA EL5 sing 111 n n CHD C1D EL5 doub 112 e n CHD C4C EL5 sing 113 n n C3A C4A EL5 sing 114 n n C1D C2D EL5 sing 115 n n C3D CAD EL5 sing 116 n n C3D C2D EL5 doub 117 n n CMC C3C EL5 sing 118 n n NA C4A EL5 sing 119 n n C4A CHB EL5 doub 120 z n C4C C3C EL5 doub 121 n y C4C NC EL5 sing 122 n y C2D CMD EL5 sing 123 n n C3C C2C EL5 sing 124 n y NC C1C EL5 sing 125 n y CHB C1B EL5 sing 126 n n C2C C1C EL5 doub 127 n y C2C CAC EL5 sing 128 n n NB C1B EL5 doub 129 n n NB C4B EL5 sing 130 n n C1C CHC EL5 sing 131 n n C1B C2B EL5 sing 132 n n CAC CBC EL5 sing 133 n n C4B CHC EL5 doub 134 z n C4B C3B EL5 sing 135 n n C2B C3B EL5 doub 136 n n C2B CMB EL5 sing 137 n n O1C CGC EL5 doub 138 n n C3B CAB EL5 sing 139 n n CBC CGC EL5 sing 140 n n CGC O2C EL5 sing 141 n n CAB CBB EL5 sing 142 n n CBB CGB EL5 sing 143 n n CGB O2B EL5 doub 144 n n CGB O1B EL5 sing 145 n n O1B H1 EL5 sing 146 n n C2A H2 EL5 sing 147 n n O2C H3 EL5 sing 148 n n CAA H4 EL5 sing 149 n n CAB H6 EL5 sing 150 n n CAB H7 EL5 sing 151 n n CAC H8 EL5 sing 152 n n CAC H9 EL5 sing 153 n n CAD H10 EL5 sing 154 n n CBA H12 EL5 sing 155 n n CBA H13 EL5 sing 156 n n CBA H14 EL5 sing 157 n n CBB H15 EL5 sing 158 n n CBB H16 EL5 sing 159 n n CBC H17 EL5 sing 160 n n CBC H18 EL5 sing 161 n n CBD H19 EL5 sing 162 n n CBD H20 EL5 sing 163 n n CHB H22 EL5 sing 164 n n CHC H24 EL5 sing 165 n n CHD H26 EL5 sing 166 n n CMA H28 EL5 sing 167 n n CMA H29 EL5 sing 168 n n CMA H30 EL5 sing 169 n n CMB H31 EL5 sing 170 n n CMB H32 EL5 sing 171 n n CMB H33 EL5 sing 172 n n CMC H34 EL5 sing 173 n n CMC H35 EL5 sing 174 n n CMC H36 EL5 sing 175 n n CMD H37 EL5 sing 176 n n CMD H38 EL5 sing 177 n n CMD H39 EL5 sing 178 n n NA H40 EL5 sing 179 n n NC H42 EL5 sing 180 n n ND H5 EL5 sing 181 n n # _atom_sites.entry_id 6PTQ _atom_sites.fract_transf_matrix[1][1] 0.011949 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003797 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01199 _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] 0.012079 _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 EL5 A 1 501 522 EL5 BLA . D 3 BEN B 1 601 601 BEN BEN . E 2 EL5 B 1 602 522 EL5 BLA . F 4 HOH A 1 601 30 HOH HOH . F 4 HOH A 2 602 28 HOH HOH . F 4 HOH A 3 603 119 HOH HOH . F 4 HOH A 4 604 92 HOH HOH . F 4 HOH A 5 605 35 HOH HOH . F 4 HOH A 6 606 62 HOH HOH . F 4 HOH A 7 607 61 HOH HOH . F 4 HOH A 8 608 6 HOH HOH . F 4 HOH A 9 609 94 HOH HOH . F 4 HOH A 10 610 60 HOH HOH . F 4 HOH A 11 611 25 HOH HOH . F 4 HOH A 12 612 116 HOH HOH . F 4 HOH A 13 613 65 HOH HOH . F 4 HOH A 14 614 8 HOH HOH . F 4 HOH A 15 615 46 HOH HOH . F 4 HOH A 16 616 44 HOH HOH . F 4 HOH A 17 617 103 HOH HOH . F 4 HOH A 18 618 22 HOH HOH . F 4 HOH A 19 619 112 HOH HOH . F 4 HOH A 20 620 97 HOH HOH . F 4 HOH A 21 621 27 HOH HOH . F 4 HOH A 22 622 105 HOH HOH . F 4 HOH A 23 623 64 HOH HOH . F 4 HOH A 24 624 33 HOH HOH . F 4 HOH A 25 625 63 HOH HOH . F 4 HOH A 26 626 80 HOH HOH . F 4 HOH A 27 627 96 HOH HOH . F 4 HOH A 28 628 1 HOH HOH . F 4 HOH A 29 629 2 HOH HOH . F 4 HOH A 30 630 122 HOH HOH . F 4 HOH A 31 631 24 HOH HOH . F 4 HOH A 32 632 36 HOH HOH . F 4 HOH A 33 633 73 HOH HOH . F 4 HOH A 34 634 42 HOH HOH . F 4 HOH A 35 635 14 HOH HOH . F 4 HOH A 36 636 26 HOH HOH . F 4 HOH A 37 637 7 HOH HOH . F 4 HOH A 38 638 57 HOH HOH . F 4 HOH A 39 639 106 HOH HOH . F 4 HOH A 40 640 82 HOH HOH . F 4 HOH A 41 641 18 HOH HOH . F 4 HOH A 42 642 19 HOH HOH . F 4 HOH A 43 643 15 HOH HOH . F 4 HOH A 44 644 20 HOH HOH . F 4 HOH A 45 645 32 HOH HOH . F 4 HOH A 46 646 21 HOH HOH . F 4 HOH A 47 647 11 HOH HOH . F 4 HOH A 48 648 58 HOH HOH . F 4 HOH A 49 649 102 HOH HOH . F 4 HOH A 50 650 118 HOH HOH . F 4 HOH A 51 651 37 HOH HOH . F 4 HOH A 52 652 115 HOH HOH . F 4 HOH A 53 653 101 HOH HOH . F 4 HOH A 54 654 23 HOH HOH . F 4 HOH A 55 655 31 HOH HOH . F 4 HOH A 56 656 88 HOH HOH . F 4 HOH A 57 657 39 HOH HOH . F 4 HOH A 58 658 113 HOH HOH . F 4 HOH A 59 659 117 HOH HOH . F 4 HOH A 60 660 75 HOH HOH . F 4 HOH A 61 661 98 HOH HOH . F 4 HOH A 62 662 95 HOH HOH . F 4 HOH A 63 663 72 HOH HOH . F 4 HOH A 64 664 81 HOH HOH . F 4 HOH A 65 665 86 HOH HOH . F 4 HOH A 66 666 40 HOH HOH . F 4 HOH A 67 667 107 HOH HOH . F 4 HOH A 68 668 89 HOH HOH . F 4 HOH A 69 669 38 HOH HOH . G 4 HOH B 1 701 84 HOH HOH . G 4 HOH B 2 702 85 HOH HOH . G 4 HOH B 3 703 59 HOH HOH . G 4 HOH B 4 704 111 HOH HOH . G 4 HOH B 5 705 66 HOH HOH . G 4 HOH B 6 706 55 HOH HOH . G 4 HOH B 7 707 13 HOH HOH . G 4 HOH B 8 708 53 HOH HOH . G 4 HOH B 9 709 4 HOH HOH . G 4 HOH B 10 710 69 HOH HOH . G 4 HOH B 11 711 48 HOH HOH . G 4 HOH B 12 712 45 HOH HOH . G 4 HOH B 13 713 5 HOH HOH . G 4 HOH B 14 714 74 HOH HOH . G 4 HOH B 15 715 51 HOH HOH . G 4 HOH B 16 716 17 HOH HOH . G 4 HOH B 17 717 110 HOH HOH . G 4 HOH B 18 718 3 HOH HOH . G 4 HOH B 19 719 29 HOH HOH . G 4 HOH B 20 720 54 HOH HOH . G 4 HOH B 21 721 9 HOH HOH . G 4 HOH B 22 722 52 HOH HOH . G 4 HOH B 23 723 123 HOH HOH . G 4 HOH B 24 724 68 HOH HOH . G 4 HOH B 25 725 12 HOH HOH . G 4 HOH B 26 726 50 HOH HOH . G 4 HOH B 27 727 49 HOH HOH . G 4 HOH B 28 728 67 HOH HOH . G 4 HOH B 29 729 124 HOH HOH . G 4 HOH B 30 730 16 HOH HOH . G 4 HOH B 31 731 91 HOH HOH . G 4 HOH B 32 732 43 HOH HOH . G 4 HOH B 33 733 34 HOH HOH . G 4 HOH B 34 734 71 HOH HOH . G 4 HOH B 35 735 77 HOH HOH . G 4 HOH B 36 736 121 HOH HOH . G 4 HOH B 37 737 104 HOH HOH . G 4 HOH B 38 738 10 HOH HOH . G 4 HOH B 39 739 120 HOH HOH . G 4 HOH B 40 740 79 HOH HOH . G 4 HOH B 41 741 78 HOH HOH . G 4 HOH B 42 742 100 HOH HOH . G 4 HOH B 43 743 41 HOH HOH . G 4 HOH B 44 744 56 HOH HOH . G 4 HOH B 45 745 87 HOH HOH . G 4 HOH B 46 746 70 HOH HOH . G 4 HOH B 47 747 99 HOH HOH . G 4 HOH B 48 748 109 HOH HOH . G 4 HOH B 49 749 108 HOH HOH . G 4 HOH B 50 750 114 HOH HOH . G 4 HOH B 51 751 76 HOH HOH . G 4 HOH B 52 752 93 HOH HOH . G 4 HOH B 53 753 90 HOH HOH . G 4 HOH B 54 754 47 HOH HOH . G 4 HOH B 55 755 83 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 C1A EL5 . . . C 2 -35.866 4.02 6.985 1 45.63 ? C1A EL5 501 A 1 HETATM 2 C C1B EL5 . . . C 2 -32.984 5.238 3.588 1 35.22 ? C1B EL5 501 A 1 HETATM 3 O O1B EL5 . . . C 2 -27.626 4.849 -0.487 1 43.95 ? O1B EL5 501 A 1 HETATM 4 C C1C EL5 . . . C 2 -31.496 1.051 2.196 1 42.23 ? C1C EL5 501 A 1 HETATM 5 O O1C EL5 . . . C 2 -27.769 -2.305 1.21 1 38.35 ? O1C EL5 501 A 1 HETATM 6 C C1D EL5 . . . C 2 -33.536 -2.832 3.783 1 38.51 ? C1D EL5 501 A 1 HETATM 7 C C2A EL5 . . . C 2 -36.464 5.4 7.114 1 45.88 ? C2A EL5 501 A 1 HETATM 8 C C2B EL5 . . . C 2 -32.13 5.981 2.66 1 37.61 ? C2B EL5 501 A 1 HETATM 9 O O2B EL5 . . . C 2 -27.395 6.639 0.799 1 43.47 ? O2B EL5 501 A 1 HETATM 10 C C2C EL5 . . . C 2 -30.907 -0.04 1.583 1 41.72 ? C2C EL5 501 A 1 HETATM 11 O O2C EL5 . . . C 2 -27.834 -1.42 3.163 1 39.26 ? O2C EL5 501 A 1 HETATM 12 C C2D EL5 . . . C 2 -34.661 -3.787 3.911 1 42.06 ? C2D EL5 501 A 1 HETATM 13 C C3A EL5 . . . C 2 -35.725 6.301 6.116 1 48.62 ? C3A EL5 501 A 1 HETATM 14 C C3B EL5 . . . C 2 -31.327 4.984 1.974 1 41.85 ? C3B EL5 501 A 1 HETATM 15 C C3C EL5 . . . C 2 -31.592 -1.135 1.966 1 41.33 ? C3C EL5 501 A 1 HETATM 16 C C3D EL5 . . . C 2 -34.165 -5.091 4.198 1 45.03 ? C3D EL5 501 A 1 HETATM 17 C C4A EL5 . . . C 2 -34.718 5.505 5.381 1 41.4 ? C4A EL5 501 A 1 HETATM 18 C C4B EL5 . . . C 2 -31.648 3.582 2.49 1 40.74 ? C4B EL5 501 A 1 HETATM 19 C C4C EL5 . . . C 2 -32.593 -0.714 2.814 1 43.27 ? C4C EL5 501 A 1 HETATM 20 C C4D EL5 . . . C 2 -32.678 -5.063 4.3 1 41.91 ? C4D EL5 501 A 1 HETATM 21 C CAA EL5 . . . C 2 -35.89 7.596 5.873 1 47.97 ? CAA EL5 501 A 1 HETATM 22 C CAB EL5 . . . C 2 -30.283 5.258 0.918 1 40.53 ? CAB EL5 501 A 1 HETATM 23 C CAC EL5 . . . C 2 -29.706 -0.005 0.628 1 39.01 ? CAC EL5 501 A 1 HETATM 24 C CAD EL5 . . . C 2 -35.014 -6.344 4.385 1 43.12 ? CAD EL5 501 A 1 HETATM 25 C CBA EL5 . . . C 2 -36.604 8.524 6.815 1 54.87 ? CBA EL5 501 A 1 HETATM 26 C CBB EL5 . . . C 2 -28.942 4.948 1.545 1 41.07 ? CBB EL5 501 A 1 HETATM 27 C CBC EL5 . . . C 2 -28.347 0.058 1.322 1 36.49 ? CBC EL5 501 A 1 HETATM 28 C CBD EL5 . . . C 2 -34.543 -7.382 5.056 1 46.75 ? CBD EL5 501 A 1 HETATM 29 C CGB EL5 . . . C 2 -27.919 5.509 0.561 1 49.59 ? CGB EL5 501 A 1 HETATM 30 C CGC EL5 . . . C 2 -27.959 -1.296 1.923 1 39.01 ? CGC EL5 501 A 1 HETATM 31 C CHB EL5 . . . C 2 -33.953 5.998 4.456 1 45.37 ? CHB EL5 501 A 1 HETATM 32 C CHC EL5 . . . C 2 -31.04 2.494 2.053 1 39.17 ? CHC EL5 501 A 1 HETATM 33 C CHD EL5 . . . C 2 -33.656 -1.557 3.52 1 50.86 ? CHD EL5 501 A 1 HETATM 34 C CMA EL5 . . . C 2 -36.309 5.921 8.546 1 51.16 ? CMA EL5 501 A 1 HETATM 35 C CMB EL5 . . . C 2 -32.133 7.504 2.469 1 36.91 ? CMB EL5 501 A 1 HETATM 36 C CMC EL5 . . . C 2 -31.311 -2.584 1.525 1 45.11 ? CMC EL5 501 A 1 HETATM 37 C CMD EL5 . . . C 2 -36.123 -3.388 3.728 1 38.34 ? CMD EL5 501 A 1 HETATM 38 N NA EL5 . . . C 2 -34.792 4.08 5.899 1 44.86 ? NA EL5 501 A 1 HETATM 39 O OA EL5 . . . C 2 -36.147 3.037 7.577 1 43.89 ? OA EL5 501 A 1 HETATM 40 N NB EL5 . . . C 2 -32.709 3.786 3.534 1 38.61 ? NB EL5 501 A 1 HETATM 41 N NC EL5 . . . C 2 -32.518 0.621 2.959 1 41.04 ? NC EL5 501 A 1 HETATM 42 N ND EL5 . . . C 2 -32.262 -3.619 4.033 1 42.37 ? ND EL5 501 A 1 HETATM 43 O OD EL5 . . . C 2 -31.961 -5.958 4.528 1 40.46 ? OD EL5 501 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #