data_3ZJ4 # _model_server_result.job_id FBjtZuibWmSXeBlYDeSCYg _model_server_result.datetime_utc '2024-11-08 15:11:49' _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 3zj4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":4000}' # _entry.id 3ZJ4 # _exptl.entry_id 3ZJ4 _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 82.08 _cell.angle_beta 82.48 _cell.angle_gamma 62.33 _cell.entry_id 3ZJ4 _cell.length_a 85.445 _cell.length_b 88.207 _cell.length_c 104.398 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZJ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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 E N N ? 2 F N N ? 2 G N N ? 2 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 metalc ? metalc1 A OH TYR 416 A TYR 389 1_555 E FE HEM . A HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 B OH TYR 416 B TYR 389 1_555 F FE HEM . B HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 C OH TYR 416 C TYR 389 1_555 G FE HEM . C HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc4 D OH TYR 416 D TYR 389 1_555 H FE HEM . D HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? # _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 3ZJ4 _atom_sites.fract_transf_matrix[1][1] 0.011703 _atom_sites.fract_transf_matrix[1][2] -0.006137 _atom_sites.fract_transf_matrix[1][3] -0.001011 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012801 _atom_sites.fract_transf_matrix[2][3] -0.001127 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009699 _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 4000 4000 HEM HEM . F 2 HEM B 1 4000 4000 HEM HEM . G 2 HEM C 1 4000 4000 HEM HEM . H 2 HEM D 1 4000 4000 HEM HEM . # 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 . . . F 2 14.14 1.284 -80.124 1 35.7 ? CHA HEM 4000 B 1 HETATM 2 C CHB HEM . . . F 2 16.107 -1.99 -83.126 1 39.74 ? CHB HEM 4000 B 1 HETATM 3 C CHC HEM . . . F 2 19.641 -2.775 -79.918 1 38.6 ? CHC HEM 4000 B 1 HETATM 4 C CHD HEM . . . F 2 16.995 -0.522 -76.561 1 34.26 ? CHD HEM 4000 B 1 HETATM 5 C C1A HEM . . . F 2 14.392 0.522 -81.249 1 31.71 ? C1A HEM 4000 B 1 HETATM 6 C C2A HEM . . . F 2 13.707 0.591 -82.528 1 43.19 ? C2A HEM 4000 B 1 HETATM 7 C C3A HEM . . . F 2 14.254 -0.306 -83.348 1 44.43 ? C3A HEM 4000 B 1 HETATM 8 C C4A HEM . . . F 2 15.305 -0.988 -82.627 1 33.06 ? C4A HEM 4000 B 1 HETATM 9 C CMA HEM . . . F 2 13.831 -0.57 -84.809 1 44.77 ? CMA HEM 4000 B 1 HETATM 10 C CAA HEM . . . F 2 12.553 1.534 -82.922 1 43.6 ? CAA HEM 4000 B 1 HETATM 11 C CBA HEM . . . F 2 11.214 1.085 -82.355 1 39.29 ? CBA HEM 4000 B 1 HETATM 12 C CGA HEM . . . F 2 10.182 1.999 -82.957 1 43.71 ? CGA HEM 4000 B 1 HETATM 13 O O1A HEM . . . F 2 9.157 2.288 -82.288 1 29.34 ? O1A HEM 4000 B 1 HETATM 14 O O2A HEM . . . F 2 10.408 2.454 -84.108 1 43.28 ? O2A HEM 4000 B 1 HETATM 15 C C1B HEM . . . F 2 17.186 -2.549 -82.479 1 51.63 ? C1B HEM 4000 B 1 HETATM 16 C C2B HEM . . . F 2 17.899 -3.735 -82.9 1 32.28 ? C2B HEM 4000 B 1 HETATM 17 C C3B HEM . . . F 2 18.888 -3.966 -82.018 1 36.85 ? C3B HEM 4000 B 1 HETATM 18 C C4B HEM . . . F 2 18.821 -2.921 -81.014 1 37.69 ? C4B HEM 4000 B 1 HETATM 19 C CMB HEM . . . F 2 17.509 -4.53 -84.164 1 32.99 ? CMB HEM 4000 B 1 HETATM 20 C CAB HEM . . . F 2 19.948 -5.099 -81.984 1 44.61 ? CAB HEM 4000 B 1 HETATM 21 C CBB HEM . . . F 2 20.017 -6.109 -82.859 1 40.44 ? CBB HEM 4000 B 1 HETATM 22 C C1C HEM . . . F 2 19.169 -2.371 -78.691 1 37.12 ? C1C HEM 4000 B 1 HETATM 23 C C2C HEM . . . F 2 19.64 -2.797 -77.388 1 35.19 ? C2C HEM 4000 B 1 HETATM 24 C C3C HEM . . . F 2 18.903 -2.165 -76.455 1 37.51 ? C3C HEM 4000 B 1 HETATM 25 C C4C HEM . . . F 2 17.94 -1.331 -77.152 1 37.74 ? C4C HEM 4000 B 1 HETATM 26 C CMC HEM . . . F 2 20.8 -3.798 -77.183 1 47.72 ? CMC HEM 4000 B 1 HETATM 27 C CAC HEM . . . F 2 18.97 -2.244 -74.906 1 45.93 ? CAC HEM 4000 B 1 HETATM 28 C CBC HEM . . . F 2 19.736 -3.09 -74.208 1 58.47 ? CBC HEM 4000 B 1 HETATM 29 C C1D HEM . . . F 2 16.021 0.222 -77.198 1 30.52 ? C1D HEM 4000 B 1 HETATM 30 C C2D HEM . . . F 2 15.146 1.161 -76.539 1 30.1 ? C2D HEM 4000 B 1 HETATM 31 C C3D HEM . . . F 2 14.242 1.732 -77.638 1 29.37 ? C3D HEM 4000 B 1 HETATM 32 C C4D HEM . . . F 2 14.668 1.079 -78.863 1 31.66 ? C4D HEM 4000 B 1 HETATM 33 C CMD HEM . . . F 2 15.129 1.497 -75.033 1 26.95 ? CMD HEM 4000 B 1 HETATM 34 C CAD HEM . . . F 2 13.129 2.789 -77.449 1 32.49 ? CAD HEM 4000 B 1 HETATM 35 C CBD HEM . . . F 2 11.767 2.226 -77.841 1 25.24 ? CBD HEM 4000 B 1 HETATM 36 C CGD HEM . . . F 2 10.691 3.156 -77.344 1 29.64 ? CGD HEM 4000 B 1 HETATM 37 O O1D HEM . . . F 2 9.49 2.827 -77.522 1 30.79 ? O1D HEM 4000 B 1 HETATM 38 O O2D HEM . . . F 2 11.036 4.221 -76.768 1 27.33 ? O2D HEM 4000 B 1 HETATM 39 N NA HEM . . . F 2 15.36 -0.459 -81.352 1 28.06 ? NA HEM 4000 B 1 HETATM 40 N NB HEM . . . F 2 17.773 -2.078 -81.325 1 36.62 ? NB HEM 4000 B 1 HETATM 41 N NC HEM . . . F 2 18.132 -1.481 -78.508 1 37.36 ? NC HEM 4000 B 1 HETATM 42 N ND HEM . . . F 2 15.71 0.206 -78.556 1 28.85 ? ND HEM 4000 B 1 HETATM 43 FE FE HEM . . . F 2 16.811 -0.86 -79.976 1 38.7 ? FE HEM 4000 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #