data_5B2V # _model_server_result.job_id ZH7zYv0mZ1peudSzpkaT8g _model_server_result.datetime_utc '2024-11-25 10:56:47' _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 5b2v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5B2V # _exptl.entry_id 5B2V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _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 98.23 _cell.angle_gamma 90 _cell.entry_id 5B2V _cell.length_a 58.881 _cell.length_b 147.491 _cell.length_c 64.247 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B2V _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,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 # 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 metalc ? metalc1 A SG CYS 401 A CYS 400 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc2 B SG CYS 401 B CYS 400 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 5B2V _atom_sites.fract_transf_matrix[1][1] 0.016983 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002457 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00678 _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] 0.015727 _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 HEM A 1 501 501 HEM HEM . D 3 W06 A 1 502 502 W06 W06 . E 2 HEM B 1 501 501 HEM HEM . F 3 W06 B 1 502 502 W06 W06 . G 4 HOH A 1 601 75 HOH HOH . G 4 HOH A 2 602 72 HOH HOH . G 4 HOH A 3 603 63 HOH HOH . G 4 HOH A 4 604 24 HOH HOH . G 4 HOH A 5 605 90 HOH HOH . G 4 HOH A 6 606 12 HOH HOH . G 4 HOH A 7 607 61 HOH HOH . G 4 HOH A 8 608 40 HOH HOH . G 4 HOH A 9 609 128 HOH HOH . G 4 HOH A 10 610 83 HOH HOH . G 4 HOH A 11 611 78 HOH HOH . G 4 HOH A 12 612 67 HOH HOH . G 4 HOH A 13 613 39 HOH HOH . G 4 HOH A 14 614 68 HOH HOH . G 4 HOH A 15 615 47 HOH HOH . G 4 HOH A 16 616 36 HOH HOH . G 4 HOH A 17 617 99 HOH HOH . G 4 HOH A 18 618 30 HOH HOH . G 4 HOH A 19 619 88 HOH HOH . G 4 HOH A 20 620 8 HOH HOH . G 4 HOH A 21 621 22 HOH HOH . G 4 HOH A 22 622 56 HOH HOH . G 4 HOH A 23 623 34 HOH HOH . G 4 HOH A 24 624 48 HOH HOH . G 4 HOH A 25 625 71 HOH HOH . G 4 HOH A 26 626 1 HOH HOH . G 4 HOH A 27 627 9 HOH HOH . G 4 HOH A 28 628 50 HOH HOH . G 4 HOH A 29 629 62 HOH HOH . G 4 HOH A 30 630 116 HOH HOH . G 4 HOH A 31 631 110 HOH HOH . G 4 HOH A 32 632 15 HOH HOH . G 4 HOH A 33 633 4 HOH HOH . G 4 HOH A 34 634 87 HOH HOH . G 4 HOH A 35 635 5 HOH HOH . G 4 HOH A 36 636 38 HOH HOH . G 4 HOH A 37 637 20 HOH HOH . G 4 HOH A 38 638 23 HOH HOH . G 4 HOH A 39 639 112 HOH HOH . G 4 HOH A 40 640 121 HOH HOH . G 4 HOH A 41 641 51 HOH HOH . G 4 HOH A 42 642 122 HOH HOH . G 4 HOH A 43 643 104 HOH HOH . G 4 HOH A 44 644 45 HOH HOH . G 4 HOH A 45 645 113 HOH HOH . G 4 HOH A 46 646 69 HOH HOH . G 4 HOH A 47 647 19 HOH HOH . G 4 HOH A 48 648 59 HOH HOH . G 4 HOH A 49 649 100 HOH HOH . G 4 HOH A 50 650 25 HOH HOH . G 4 HOH A 51 651 106 HOH HOH . G 4 HOH A 52 652 95 HOH HOH . G 4 HOH A 53 653 43 HOH HOH . G 4 HOH A 54 654 10 HOH HOH . G 4 HOH A 55 655 13 HOH HOH . G 4 HOH A 56 656 16 HOH HOH . G 4 HOH A 57 657 74 HOH HOH . G 4 HOH A 58 658 102 HOH HOH . G 4 HOH A 59 659 28 HOH HOH . G 4 HOH A 60 660 2 HOH HOH . G 4 HOH A 61 661 21 HOH HOH . G 4 HOH A 62 662 129 HOH HOH . G 4 HOH A 63 663 97 HOH HOH . G 4 HOH A 64 664 117 HOH HOH . G 4 HOH A 65 665 64 HOH HOH . G 4 HOH A 66 666 98 HOH HOH . G 4 HOH A 67 667 11 HOH HOH . G 4 HOH A 68 668 80 HOH HOH . G 4 HOH A 69 669 105 HOH HOH . G 4 HOH A 70 670 70 HOH HOH . H 4 HOH B 1 601 27 HOH HOH . H 4 HOH B 2 602 89 HOH HOH . H 4 HOH B 3 603 7 HOH HOH . H 4 HOH B 4 604 65 HOH HOH . H 4 HOH B 5 605 115 HOH HOH . H 4 HOH B 6 606 86 HOH HOH . H 4 HOH B 7 607 3 HOH HOH . H 4 HOH B 8 608 109 HOH HOH . H 4 HOH B 9 609 18 HOH HOH . H 4 HOH B 10 610 58 HOH HOH . H 4 HOH B 11 611 76 HOH HOH . H 4 HOH B 12 612 111 HOH HOH . H 4 HOH B 13 613 6 HOH HOH . H 4 HOH B 14 614 52 HOH HOH . H 4 HOH B 15 615 114 HOH HOH . H 4 HOH B 16 616 26 HOH HOH . H 4 HOH B 17 617 49 HOH HOH . H 4 HOH B 18 618 53 HOH HOH . H 4 HOH B 19 619 84 HOH HOH . H 4 HOH B 20 620 85 HOH HOH . H 4 HOH B 21 621 60 HOH HOH . H 4 HOH B 22 622 94 HOH HOH . H 4 HOH B 23 623 96 HOH HOH . H 4 HOH B 24 624 44 HOH HOH . H 4 HOH B 25 625 42 HOH HOH . H 4 HOH B 26 626 124 HOH HOH . H 4 HOH B 27 627 118 HOH HOH . H 4 HOH B 28 628 35 HOH HOH . H 4 HOH B 29 629 103 HOH HOH . H 4 HOH B 30 630 119 HOH HOH . H 4 HOH B 31 631 91 HOH HOH . H 4 HOH B 32 632 41 HOH HOH . H 4 HOH B 33 633 123 HOH HOH . H 4 HOH B 34 634 14 HOH HOH . H 4 HOH B 35 635 107 HOH HOH . H 4 HOH B 36 636 66 HOH HOH . H 4 HOH B 37 637 73 HOH HOH . H 4 HOH B 38 638 126 HOH HOH . H 4 HOH B 39 639 57 HOH HOH . H 4 HOH B 40 640 32 HOH HOH . H 4 HOH B 41 641 125 HOH HOH . H 4 HOH B 42 642 82 HOH HOH . H 4 HOH B 43 643 37 HOH HOH . H 4 HOH B 44 644 54 HOH HOH . H 4 HOH B 45 645 101 HOH HOH . H 4 HOH B 46 646 92 HOH HOH . H 4 HOH B 47 647 81 HOH HOH . H 4 HOH B 48 648 108 HOH HOH . H 4 HOH B 49 649 17 HOH HOH . H 4 HOH B 50 650 79 HOH HOH . H 4 HOH B 51 651 33 HOH HOH . H 4 HOH B 52 652 55 HOH HOH . H 4 HOH B 53 653 93 HOH HOH . H 4 HOH B 54 654 77 HOH HOH . H 4 HOH B 55 655 127 HOH HOH . H 4 HOH B 56 656 31 HOH HOH . H 4 HOH B 57 657 29 HOH HOH . H 4 HOH B 58 658 46 HOH HOH . H 4 HOH B 59 659 120 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 . . . C 2 -2.807 -3.061 14.705 1 35.03 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 2.013 -2.958 14.328 1 35.15 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 1.716 1.215 11.832 1 35.27 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 -3.051 1.314 12.637 1 35.67 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 -1.488 -3.4 14.769 1 34.74 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 -0.992 -4.584 15.359 1 34.7 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 0.363 -4.546 15.26 1 34.43 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 0.706 -3.341 14.611 1 34.55 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 1.34 -5.599 15.738 1 34.17 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 -1.816 -5.687 15.987 1 34.76 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 -2.105 -5.298 17.442 1 35.13 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 -2.66 -6.435 18.268 1 35.84 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 -2.852 -6.246 19.491 1 35.8 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 -2.938 -7.549 17.761 1 35.44 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 2.366 -1.808 13.601 1 34.98 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 3.702 -1.485 13.214 1 35.4 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 3.644 -0.31 12.501 1 35.59 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 2.207 0.065 12.466 1 35.42 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 4.938 -2.29 13.545 1 35.51 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 4.72 0.492 11.868 1 36.09 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 6.017 0.188 11.883 1 36.95 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 0.378 1.622 11.817 1 35.81 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 -0.116 2.795 11.206 1 36.5 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 -1.49 2.831 11.446 1 36.62 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 -1.807 1.665 12.205 1 36.06 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 0.71 3.814 10.443 1 36.6 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 -2.503 3.827 11.02 1 37.2 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 -2.253 4.899 10.275 1 38.15 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 -3.299 0.098 13.263 1 35.2 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 -4.684 -0.273 13.591 1 35.21 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 -4.621 -1.482 14.161 1 35.06 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 -3.196 -1.848 14.17 1 35.13 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 -5.944 0.527 13.362 1 35.54 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 -5.794 -2.286 14.676 1 34.66 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 -6.228 -3.299 13.614 1 34.95 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 -7.546 -3.949 13.982 1 34.9 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 -7.653 -4.593 15.05 1 34.56 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 -8.536 -3.862 13.22 1 33.69 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 -0.443 -2.636 14.335 1 34.46 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 1.538 -0.878 13.133 1 35.16 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 -0.662 0.963 12.424 1 35.62 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 -2.428 -0.876 13.616 1 35.21 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 -0.534 -0.871 13.407 1 35.01 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 43 #