data_3SWZ # _model_server_result.job_id NvDJpTT3LPsznX4Nvhqw_A _model_server_result.datetime_utc '2024-10-12 06:26:02' _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 3swz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 3SWZ # _exptl.entry_id 3SWZ _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 4 _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 3SWZ _cell.length_a 91.415 _cell.length_b 152.09 _cell.length_c 167.656 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SWZ _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,M 1 1 B,G,H,N 2 1 C,I,J,O 3 1 D,K,L,P 4 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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 424 A CYS 442 1_555 E FE HEM . A HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc2 E FE HEM . A HEM 600 1_555 F N51 TOK . A TOK 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc3 B SG CYS 424 B CYS 442 1_555 G FE HEM . B HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc4 G FE HEM . B HEM 600 1_555 H N51 TOK . B TOK 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 C SG CYS 424 C CYS 442 1_555 I FE HEM . C HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc6 I FE HEM . C HEM 600 1_555 J N51 TOK . C TOK 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc7 D SG CYS 424 D CYS 442 1_555 K FE HEM . D HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc8 K FE HEM . D HEM 600 1_555 L N51 TOK . D TOK 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? # _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 3SWZ _atom_sites.fract_transf_matrix[1][1] 0.010939 _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] 0.006575 _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] 0.005965 _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 E 2 HEM A 1 600 600 HEM HEM . F 3 TOK A 1 601 601 TOK TOK . G 2 HEM B 1 600 600 HEM HEM . H 3 TOK B 1 601 601 TOK TOK . I 2 HEM C 1 600 600 HEM HEM . J 3 TOK C 1 601 601 TOK TOK . K 2 HEM D 1 600 600 HEM HEM . L 3 TOK D 1 601 601 TOK TOK . M 4 HOH A 1 4 4 HOH HOH . M 4 HOH A 2 5 5 HOH HOH . M 4 HOH A 3 6 6 HOH HOH . M 4 HOH A 4 11 11 HOH HOH . M 4 HOH A 5 12 12 HOH HOH . M 4 HOH A 6 14 14 HOH HOH . M 4 HOH A 7 513 513 HOH HOH . M 4 HOH A 8 514 514 HOH HOH . M 4 HOH A 9 515 515 HOH HOH . M 4 HOH A 10 516 516 HOH HOH . M 4 HOH A 11 517 517 HOH HOH . M 4 HOH A 12 518 518 HOH HOH . M 4 HOH A 13 519 519 HOH HOH . M 4 HOH A 14 520 520 HOH HOH . M 4 HOH A 15 521 521 HOH HOH . M 4 HOH A 16 522 522 HOH HOH . M 4 HOH A 17 523 523 HOH HOH . M 4 HOH A 18 524 524 HOH HOH . M 4 HOH A 19 525 525 HOH HOH . M 4 HOH A 20 526 526 HOH HOH . M 4 HOH A 21 527 527 HOH HOH . M 4 HOH A 22 528 528 HOH HOH . M 4 HOH A 23 529 529 HOH HOH . M 4 HOH A 24 530 530 HOH HOH . M 4 HOH A 25 531 531 HOH HOH . M 4 HOH A 26 532 532 HOH HOH . N 4 HOH B 1 10 10 HOH HOH . N 4 HOH B 2 17 17 HOH HOH . N 4 HOH B 3 18 18 HOH HOH . N 4 HOH B 4 513 513 HOH HOH . N 4 HOH B 5 514 514 HOH HOH . N 4 HOH B 6 515 515 HOH HOH . N 4 HOH B 7 516 516 HOH HOH . N 4 HOH B 8 517 517 HOH HOH . N 4 HOH B 9 518 518 HOH HOH . N 4 HOH B 10 519 519 HOH HOH . N 4 HOH B 11 520 520 HOH HOH . N 4 HOH B 12 521 521 HOH HOH . N 4 HOH B 13 522 522 HOH HOH . N 4 HOH B 14 523 523 HOH HOH . N 4 HOH B 15 524 524 HOH HOH . N 4 HOH B 16 525 525 HOH HOH . N 4 HOH B 17 526 526 HOH HOH . N 4 HOH B 18 527 527 HOH HOH . N 4 HOH B 19 528 528 HOH HOH . N 4 HOH B 20 529 529 HOH HOH . N 4 HOH B 21 530 530 HOH HOH . N 4 HOH B 22 531 531 HOH HOH . N 4 HOH B 23 532 532 HOH HOH . O 4 HOH C 1 1 1 HOH HOH . O 4 HOH C 2 2 2 HOH HOH . O 4 HOH C 3 8 8 HOH HOH . O 4 HOH C 4 13 13 HOH HOH . O 4 HOH C 5 15 15 HOH HOH . O 4 HOH C 6 16 16 HOH HOH . O 4 HOH C 7 513 513 HOH HOH . O 4 HOH C 8 514 514 HOH HOH . O 4 HOH C 9 515 515 HOH HOH . O 4 HOH C 10 516 516 HOH HOH . O 4 HOH C 11 517 517 HOH HOH . O 4 HOH C 12 518 518 HOH HOH . O 4 HOH C 13 519 519 HOH HOH . O 4 HOH C 14 520 520 HOH HOH . O 4 HOH C 15 521 521 HOH HOH . O 4 HOH C 16 522 522 HOH HOH . O 4 HOH C 17 523 523 HOH HOH . O 4 HOH C 18 524 524 HOH HOH . O 4 HOH C 19 525 525 HOH HOH . O 4 HOH C 20 526 526 HOH HOH . O 4 HOH C 21 527 527 HOH HOH . O 4 HOH C 22 528 528 HOH HOH . P 4 HOH D 1 3 3 HOH HOH . P 4 HOH D 2 7 7 HOH HOH . P 4 HOH D 3 9 9 HOH HOH . P 4 HOH D 4 513 513 HOH HOH . P 4 HOH D 5 514 514 HOH HOH . P 4 HOH D 6 515 515 HOH HOH . P 4 HOH D 7 516 516 HOH HOH . P 4 HOH D 8 517 517 HOH HOH . P 4 HOH D 9 518 518 HOH HOH . P 4 HOH D 10 519 519 HOH HOH . P 4 HOH D 11 520 520 HOH HOH . P 4 HOH D 12 521 521 HOH HOH . P 4 HOH D 13 522 522 HOH HOH . P 4 HOH D 14 523 523 HOH HOH . P 4 HOH D 15 524 524 HOH HOH . P 4 HOH D 16 525 525 HOH HOH . P 4 HOH D 17 526 526 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 . . . K 2 55.37 -20.488 18.619 1 31.74 ? CHA HEM 600 D 1 HETATM 2 C CHB HEM . . . K 2 53.974 -21.341 14.141 1 31.71 ? CHB HEM 600 D 1 HETATM 3 C CHC HEM . . . K 2 52.924 -25.809 15.44 1 27.57 ? CHC HEM 600 D 1 HETATM 4 C CHD HEM . . . K 2 55.547 -25.195 19.502 1 28 ? CHD HEM 600 D 1 HETATM 5 C C1A HEM . . . K 2 54.984 -20.31 17.322 1 32.79 ? C1A HEM 600 D 1 HETATM 6 C C2A HEM . . . K 2 54.849 -19.017 16.657 1 32.47 ? C2A HEM 600 D 1 HETATM 7 C C3A HEM . . . K 2 54.484 -19.267 15.396 1 30.13 ? C3A HEM 600 D 1 HETATM 8 C C4A HEM . . . K 2 54.373 -20.694 15.27 1 29.78 ? C4A HEM 600 D 1 HETATM 9 C CMA HEM . . . K 2 54.207 -18.235 14.272 1 27.94 ? CMA HEM 600 D 1 HETATM 10 C CAA HEM . . . K 2 55.069 -17.649 17.366 1 28.2 ? CAA HEM 600 D 1 HETATM 11 C CBA HEM . . . K 2 56.05 -16.676 16.762 1 28.44 ? CBA HEM 600 D 1 HETATM 12 C CGA HEM . . . K 2 56.27 -15.493 17.663 1 29.25 ? CGA HEM 600 D 1 HETATM 13 O O1A HEM . . . K 2 57.061 -14.625 17.258 1 34.98 ? O1A HEM 600 D 1 HETATM 14 O O2A HEM . . . K 2 55.716 -15.39 18.786 1 31.94 ? O2A HEM 600 D 1 HETATM 15 C C1B HEM . . . K 2 53.506 -22.614 14.103 1 29.78 ? C1B HEM 600 D 1 HETATM 16 C C2B HEM . . . K 2 52.833 -23.273 13.016 1 32.4 ? C2B HEM 600 D 1 HETATM 17 C C3B HEM . . . K 2 52.521 -24.517 13.383 1 32.05 ? C3B HEM 600 D 1 HETATM 18 C C4B HEM . . . K 2 53.002 -24.664 14.714 1 31.28 ? C4B HEM 600 D 1 HETATM 19 C CMB HEM . . . K 2 52.522 -22.608 11.652 1 33.67 ? CMB HEM 600 D 1 HETATM 20 C CAB HEM . . . K 2 51.846 -25.655 12.55 1 35.74 ? CAB HEM 600 D 1 HETATM 21 C CBB HEM . . . K 2 50.583 -25.792 12.158 1 32.99 ? CBB HEM 600 D 1 HETATM 22 C C1C HEM . . . K 2 53.615 -26.026 16.606 1 28.62 ? C1C HEM 600 D 1 HETATM 23 C C2C HEM . . . K 2 53.769 -27.315 17.228 1 29.15 ? C2C HEM 600 D 1 HETATM 24 C C3C HEM . . . K 2 54.47 -27.169 18.345 1 28.5 ? C3C HEM 600 D 1 HETATM 25 C C4C HEM . . . K 2 54.801 -25.766 18.483 1 29.28 ? C4C HEM 600 D 1 HETATM 26 C CMC HEM . . . K 2 53.19 -28.632 16.692 1 26.04 ? CMC HEM 600 D 1 HETATM 27 C CAC HEM . . . K 2 54.838 -28.328 19.298 1 30.7 ? CAC HEM 600 D 1 HETATM 28 C CBC HEM . . . K 2 55.882 -28.244 20.14 1 36.25 ? CBC HEM 600 D 1 HETATM 29 C C1D HEM . . . K 2 55.674 -23.866 19.711 1 28.18 ? C1D HEM 600 D 1 HETATM 30 C C2D HEM . . . K 2 56.086 -23.26 20.94 1 30.27 ? C2D HEM 600 D 1 HETATM 31 C C3D HEM . . . K 2 56.039 -21.772 20.643 1 30.94 ? C3D HEM 600 D 1 HETATM 32 C C4D HEM . . . K 2 55.577 -21.655 19.283 1 30.44 ? C4D HEM 600 D 1 HETATM 33 C CMD HEM . . . K 2 56.494 -23.942 22.287 1 30.77 ? CMD HEM 600 D 1 HETATM 34 C CAD HEM . . . K 2 56.404 -20.626 21.61 1 30.57 ? CAD HEM 600 D 1 HETATM 35 C CBD HEM . . . K 2 57.664 -19.926 21.143 1 33.42 ? CBD HEM 600 D 1 HETATM 36 C CGD HEM . . . K 2 58.334 -19.068 22.213 1 34 ? CGD HEM 600 D 1 HETATM 37 O O1D HEM . . . K 2 59.577 -19.149 22.425 1 32.77 ? O1D HEM 600 D 1 HETATM 38 O O2D HEM . . . K 2 57.634 -18.266 22.838 1 32.16 ? O2D HEM 600 D 1 HETATM 39 N NA HEM . . . K 2 54.661 -21.314 16.455 1 31.27 ? NA HEM 600 D 1 HETATM 40 N NB HEM . . . K 2 53.586 -23.466 15.138 1 32.87 ? NB HEM 600 D 1 HETATM 41 N NC HEM . . . K 2 54.258 -25.084 17.409 1 30.26 ? NC HEM 600 D 1 HETATM 42 N ND HEM . . . K 2 55.385 -22.896 18.756 1 30.9 ? ND HEM 600 D 1 HETATM 43 FE FE HEM . . . K 2 54.467 -23.141 16.956 1 30.06 ? FE HEM 600 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #