data_5WMX # _model_server_result.job_id BMBAjVVAMX_dLSpNh_fQpQ _model_server_result.datetime_utc '2024-11-01 15:34:49' _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 5wmx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 5WMX # _exptl.entry_id 5WMX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 90 _cell.angle_gamma 90 _cell.entry_id 5WMX _cell.length_a 87.057 _cell.length_b 97.566 _cell.length_c 130.416 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,F,K 1 1 B,G,H,I,J,L 2 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 ? 3 D N N ? 3 H 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 disulf ? disulf1 A SG CYS 298 A CYS 308 1_555 B SG CYS 298 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 A NE2 HIS 336 A HIS 346 1_555 D FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc2 C C CYN . A CYN 500 1_555 D FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 sing metalc ? metalc3 B NE2 HIS 336 B HIS 346 1_555 H FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc4 G C CYN . B CYN 500 1_555 H FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 sing # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 130 n n CHA C4D HEM doub 131 n n CHA HHA HEM sing 132 n n CHB C4A HEM sing 133 n n CHB C1B HEM doub 134 n n CHB HHB HEM sing 135 n n CHC C4B HEM sing 136 n n CHC C1C HEM doub 137 n n CHC HHC HEM sing 138 n n CHD C4C HEM doub 139 n n CHD C1D HEM sing 140 n n CHD HHD HEM sing 141 n n C1A C2A HEM doub 142 n y C1A NA HEM sing 143 n y C2A C3A HEM sing 144 n y C2A CAA HEM sing 145 n n C3A C4A HEM doub 146 n y C3A CMA HEM sing 147 n n C4A NA HEM sing 148 n y CMA HMA HEM sing 149 n n CMA HMAA HEM sing 150 n n CMA HMAB HEM sing 151 n n CAA CBA HEM sing 152 n n CAA HAA HEM sing 153 n n CAA HAAA HEM sing 154 n n CBA CGA HEM sing 155 n n CBA HBA HEM sing 156 n n CBA HBAA HEM sing 157 n n CGA O1A HEM doub 158 n n CGA O2A HEM sing 159 n n C1B C2B HEM sing 160 n n C1B NB HEM sing 161 n n C2B C3B HEM doub 162 n n C2B CMB HEM sing 163 n n C3B C4B HEM sing 164 n n C3B CAB HEM sing 165 n n C4B NB HEM doub 166 n n CMB HMB HEM sing 167 n n CMB HMBA HEM sing 168 n n CMB HMBB HEM sing 169 n n CAB CBB HEM doub 170 n n CAB HAB HEM sing 171 n n CBB HBB HEM sing 172 n n CBB HBBA HEM sing 173 n n C1C C2C HEM sing 174 n y C1C NC HEM sing 175 n y C2C C3C HEM doub 176 n y C2C CMC HEM sing 177 n n C3C C4C HEM sing 178 n y C3C CAC HEM sing 179 n n C4C NC HEM sing 180 n y CMC HMC HEM sing 181 n n CMC HMCA HEM sing 182 n n CMC HMCB HEM sing 183 n n CAC CBC HEM doub 184 n n CAC HAC HEM sing 185 n n CBC HBC HEM sing 186 n n CBC HBCA HEM sing 187 n n C1D C2D HEM sing 188 n n C1D ND HEM doub 189 n n C2D C3D HEM doub 190 n n C2D CMD HEM sing 191 n n C3D C4D HEM sing 192 n n C3D CAD HEM sing 193 n n C4D ND HEM sing 194 n n CMD HMD HEM sing 195 n n CMD HMDA HEM sing 196 n n CMD HMDB HEM sing 197 n n CAD CBD HEM sing 198 n n CAD HAD HEM sing 199 n n CAD HADA HEM sing 200 n n CBD CGD HEM sing 201 n n CBD HBD HEM sing 202 n n CBD HBDA HEM sing 203 n n CGD O1D HEM doub 204 n n CGD O2D HEM sing 205 n n O2A H2A HEM sing 206 n n O2D H2D HEM sing 207 n n FE NA HEM sing 208 n n FE NB HEM sing 209 n n FE NC HEM sing 210 n n FE ND HEM sing 211 n n # _atom_sites.entry_id 5WMX _atom_sites.fract_transf_matrix[1][1] 0.011487 _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] 0.010249 _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] 0.007668 _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 CYN A 1 500 500 CYN CYN . D 3 HEM A 1 501 501 HEM HEM . E 4 TRP A 1 502 502 TRP TRP . F 5 ZCW A 1 503 503 ZCW IDE . G 2 CYN B 1 500 500 CYN CYN . H 3 HEM B 1 501 501 HEM HEM . I 4 TRP B 1 502 502 TRP TRP . J 5 ZCW B 1 503 503 ZCW IDE . K 6 HOH A 1 601 94 HOH HOH . K 6 HOH A 2 602 99 HOH HOH . K 6 HOH A 3 603 53 HOH HOH . K 6 HOH A 4 604 105 HOH HOH . K 6 HOH A 5 605 48 HOH HOH . K 6 HOH A 6 606 95 HOH HOH . K 6 HOH A 7 607 6 HOH HOH . K 6 HOH A 8 608 100 HOH HOH . K 6 HOH A 9 609 81 HOH HOH . K 6 HOH A 10 610 19 HOH HOH . K 6 HOH A 11 611 60 HOH HOH . K 6 HOH A 12 612 62 HOH HOH . K 6 HOH A 13 613 110 HOH HOH . K 6 HOH A 14 614 93 HOH HOH . K 6 HOH A 15 615 82 HOH HOH . K 6 HOH A 16 616 64 HOH HOH . K 6 HOH A 17 617 102 HOH HOH . K 6 HOH A 18 618 68 HOH HOH . K 6 HOH A 19 619 101 HOH HOH . K 6 HOH A 20 620 83 HOH HOH . K 6 HOH A 21 621 34 HOH HOH . K 6 HOH A 22 622 66 HOH HOH . K 6 HOH A 23 623 40 HOH HOH . K 6 HOH A 24 624 54 HOH HOH . K 6 HOH A 25 625 91 HOH HOH . K 6 HOH A 26 626 97 HOH HOH . K 6 HOH A 27 627 89 HOH HOH . K 6 HOH A 28 628 106 HOH HOH . K 6 HOH A 29 629 71 HOH HOH . K 6 HOH A 30 630 103 HOH HOH . K 6 HOH A 31 631 104 HOH HOH . K 6 HOH A 32 632 96 HOH HOH . K 6 HOH A 33 633 10 HOH HOH . K 6 HOH A 34 634 74 HOH HOH . K 6 HOH A 35 635 51 HOH HOH . K 6 HOH A 36 636 113 HOH HOH . K 6 HOH A 37 637 77 HOH HOH . K 6 HOH A 38 638 31 HOH HOH . K 6 HOH A 39 639 21 HOH HOH . K 6 HOH A 40 640 98 HOH HOH . K 6 HOH A 41 641 1 HOH HOH . K 6 HOH A 42 642 17 HOH HOH . K 6 HOH A 43 643 22 HOH HOH . K 6 HOH A 44 644 92 HOH HOH . K 6 HOH A 45 645 5 HOH HOH . K 6 HOH A 46 646 111 HOH HOH . K 6 HOH A 47 647 42 HOH HOH . K 6 HOH A 48 648 112 HOH HOH . K 6 HOH A 49 649 44 HOH HOH . K 6 HOH A 50 650 84 HOH HOH . K 6 HOH A 51 651 70 HOH HOH . K 6 HOH A 52 652 55 HOH HOH . K 6 HOH A 53 653 37 HOH HOH . K 6 HOH A 54 654 38 HOH HOH . K 6 HOH A 55 655 90 HOH HOH . K 6 HOH A 56 656 11 HOH HOH . K 6 HOH A 57 657 4 HOH HOH . K 6 HOH A 58 658 73 HOH HOH . K 6 HOH A 59 659 109 HOH HOH . K 6 HOH A 60 660 133 HOH HOH . K 6 HOH A 61 661 20 HOH HOH . K 6 HOH A 62 662 132 HOH HOH . K 6 HOH A 63 663 18 HOH HOH . K 6 HOH A 64 664 30 HOH HOH . K 6 HOH A 65 665 3 HOH HOH . K 6 HOH A 66 666 33 HOH HOH . K 6 HOH A 67 667 107 HOH HOH . K 6 HOH A 68 668 12 HOH HOH . K 6 HOH A 69 669 108 HOH HOH . L 6 HOH B 1 601 25 HOH HOH . L 6 HOH B 2 602 115 HOH HOH . L 6 HOH B 3 603 126 HOH HOH . L 6 HOH B 4 604 121 HOH HOH . L 6 HOH B 5 605 127 HOH HOH . L 6 HOH B 6 606 114 HOH HOH . L 6 HOH B 7 607 52 HOH HOH . L 6 HOH B 8 608 15 HOH HOH . L 6 HOH B 9 609 50 HOH HOH . L 6 HOH B 10 610 8 HOH HOH . L 6 HOH B 11 611 23 HOH HOH . L 6 HOH B 12 612 26 HOH HOH . L 6 HOH B 13 613 72 HOH HOH . L 6 HOH B 14 614 123 HOH HOH . L 6 HOH B 15 615 46 HOH HOH . L 6 HOH B 16 616 116 HOH HOH . L 6 HOH B 17 617 78 HOH HOH . L 6 HOH B 18 618 120 HOH HOH . L 6 HOH B 19 619 88 HOH HOH . L 6 HOH B 20 620 9 HOH HOH . L 6 HOH B 21 621 67 HOH HOH . L 6 HOH B 22 622 124 HOH HOH . L 6 HOH B 23 623 61 HOH HOH . L 6 HOH B 24 624 59 HOH HOH . L 6 HOH B 25 625 65 HOH HOH . L 6 HOH B 26 626 57 HOH HOH . L 6 HOH B 27 627 58 HOH HOH . L 6 HOH B 28 628 56 HOH HOH . L 6 HOH B 29 629 118 HOH HOH . L 6 HOH B 30 630 43 HOH HOH . L 6 HOH B 31 631 76 HOH HOH . L 6 HOH B 32 632 45 HOH HOH . L 6 HOH B 33 633 79 HOH HOH . L 6 HOH B 34 634 125 HOH HOH . L 6 HOH B 35 635 117 HOH HOH . L 6 HOH B 36 636 14 HOH HOH . L 6 HOH B 37 637 119 HOH HOH . L 6 HOH B 38 638 47 HOH HOH . L 6 HOH B 39 639 85 HOH HOH . L 6 HOH B 40 640 75 HOH HOH . L 6 HOH B 41 641 41 HOH HOH . L 6 HOH B 42 642 87 HOH HOH . L 6 HOH B 43 643 32 HOH HOH . L 6 HOH B 44 644 63 HOH HOH . L 6 HOH B 45 645 86 HOH HOH . L 6 HOH B 46 646 131 HOH HOH . L 6 HOH B 47 647 35 HOH HOH . L 6 HOH B 48 648 39 HOH HOH . L 6 HOH B 49 649 36 HOH HOH . L 6 HOH B 50 650 28 HOH HOH . L 6 HOH B 51 651 2 HOH HOH . L 6 HOH B 52 652 122 HOH HOH . L 6 HOH B 53 653 130 HOH HOH . L 6 HOH B 54 654 13 HOH HOH . L 6 HOH B 55 655 7 HOH HOH . L 6 HOH B 56 656 69 HOH HOH . L 6 HOH B 57 657 49 HOH HOH . L 6 HOH B 58 658 129 HOH HOH . L 6 HOH B 59 659 29 HOH HOH . L 6 HOH B 60 660 24 HOH HOH . L 6 HOH B 61 661 128 HOH HOH . L 6 HOH B 62 662 27 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 CHA HEM . . . H 3 193.092 127.063 32.914 1 107.58 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . H 3 190.874 129.526 36.439 1 109.47 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . H 3 189.707 133.023 33.246 1 102.02 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . H 3 191.923 130.531 29.751 1 98.8 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . H 3 192.587 127.438 34.129 1 109.08 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . H 3 192.682 126.662 35.305 1 113 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . H 3 192.059 127.352 36.299 1 112.9 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . H 3 191.582 128.561 35.741 1 109.82 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . H 3 191.918 126.914 37.739 1 116.05 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . H 3 193.367 125.316 35.413 1 116.33 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . H 3 192.536 124.22 34.723 1 115.82 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . H 3 191.586 123.562 35.693 1 117.88 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . H 3 190.352 123.75 35.588 1 115.31 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . H 3 192.036 122.821 36.597 1 122.01 ? O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . H 3 190.352 130.704 35.875 1 106.96 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . H 3 189.61 131.676 36.618 1 107.39 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . H 3 189.265 132.677 35.741 1 105.69 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . H 3 189.833 132.268 34.424 1 103.8 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . H 3 189.272 131.617 38.091 1 109.8 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . H 3 188.504 133.938 35.96 1 106.09 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . H 3 187.998 134.394 37.11 1 108.34 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . H 3 190.211 132.666 31.994 1 100.75 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . H 3 190.034 133.394 30.8 1 99.63 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . H 3 190.663 132.703 29.773 1 99.46 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . H 3 191.231 131.526 30.376 1 99.34 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . H 3 189.308 134.712 30.617 1 99.64 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . H 3 190.653 133.22 28.371 1 100.01 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . H 3 191.125 132.627 27.272 1 100.15 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . H 3 192.399 129.394 30.39 1 100.73 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . H 3 193.126 128.378 29.608 1 100.96 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . H 3 193.456 127.412 30.483 1 102.86 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . H 3 192.924 127.85 31.786 1 104.64 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . H 3 193.437 128.419 28.122 1 99.34 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . H 3 194.22 126.139 30.177 1 103.87 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . H 3 195.719 126.359 30.402 1 106.17 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . H 3 196.329 127.187 29.295 1 105.5 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . H 3 196.227 126.824 28.098 1 103.97 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . H 3 196.942 128.244 29.577 1 106.11 ? O2D HEM 501 B 1 HETATM 39 N NA HEM . . . H 3 191.888 128.589 34.401 1 107.3 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . H 3 190.459 131.097 34.601 1 104.77 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . H 3 190.912 131.525 31.709 1 100.95 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . H 3 192.302 129.049 31.69 1 103.05 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . H 3 191.44 130.022 33.079 1 104.08 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #