data_1NZ4 # _model_server_result.job_id E2Q4CnBSWpM5c06TsoNF_Q _model_server_result.datetime_utc '2024-12-26 12:13:18' _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 1nz4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":154}' # _entry.id 1NZ4 # _exptl.entry_id 1NZ4 _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 1 _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 1NZ4 _cell.length_a 29.3 _cell.length_b 35.8 _cell.length_c 125.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NZ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NZ LYS 16 A LYS 16 1_555 C CD CD . A CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc2 A OE2 GLU 45 A GLU 45 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 A OE1 GLU 45 A GLU 45 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc4 A NE2 HIS 93 A HIS 93 1_555 D FE HEM . A HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 A NE2 HIS 113 A HIS 113 1_655 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc6 A ND1 HIS 119 A HIS 119 1_555 C CD CD . A CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.11 ? metalc ? metalc7 A OD2 ASP 122 A ASP 122 1_555 C CD CD . A CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc8 D FE HEM . A HEM 154 1_555 E O HOH . A HOH 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc9 D O2D HEM . A HEM 154 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc10 D O1D HEM . A HEM 154 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc11 E O HOH . A HOH 216 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc12 E O HOH . A HOH 217 1_555 B CD CD . A CD 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 1NZ4 _atom_sites.fract_transf_matrix[1][1] 0.03413 _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] 0.027933 _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] 0.007994 _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 B 2 CD A 1 300 300 CD CHL . C 2 CD A 1 301 301 CD CHL . D 3 HEM A 1 154 154 HEM HEM . E 4 HOH A 1 155 155 HOH HOH . E 4 HOH A 2 156 156 HOH HOH . E 4 HOH A 3 157 157 HOH HOH . E 4 HOH A 4 158 158 HOH HOH . E 4 HOH A 5 159 159 HOH HOH . E 4 HOH A 6 160 160 HOH HOH . E 4 HOH A 7 161 161 HOH HOH . E 4 HOH A 8 162 162 HOH HOH . E 4 HOH A 9 163 163 HOH HOH . E 4 HOH A 10 164 164 HOH HOH . E 4 HOH A 11 165 165 HOH HOH . E 4 HOH A 12 166 166 HOH HOH . E 4 HOH A 13 167 167 HOH HOH . E 4 HOH A 14 168 168 HOH HOH . E 4 HOH A 15 169 169 HOH HOH . E 4 HOH A 16 170 170 HOH HOH . E 4 HOH A 17 171 171 HOH HOH . E 4 HOH A 18 172 172 HOH HOH . E 4 HOH A 19 173 173 HOH HOH . E 4 HOH A 20 174 174 HOH HOH . E 4 HOH A 21 175 175 HOH HOH . E 4 HOH A 22 176 176 HOH HOH . E 4 HOH A 23 177 177 HOH HOH . E 4 HOH A 24 178 178 HOH HOH . E 4 HOH A 25 179 179 HOH HOH . E 4 HOH A 26 180 180 HOH HOH . E 4 HOH A 27 181 181 HOH HOH . E 4 HOH A 28 183 183 HOH HOH . E 4 HOH A 29 184 184 HOH HOH . E 4 HOH A 30 185 185 HOH HOH . E 4 HOH A 31 186 186 HOH HOH . E 4 HOH A 32 187 187 HOH HOH . E 4 HOH A 33 188 188 HOH HOH . E 4 HOH A 34 189 189 HOH HOH . E 4 HOH A 35 190 190 HOH HOH . E 4 HOH A 36 191 191 HOH HOH . E 4 HOH A 37 192 192 HOH HOH . E 4 HOH A 38 193 193 HOH HOH . E 4 HOH A 39 194 194 HOH HOH . E 4 HOH A 40 195 195 HOH HOH . E 4 HOH A 41 197 197 HOH HOH . E 4 HOH A 42 203 203 HOH HOH . E 4 HOH A 43 204 204 HOH HOH . E 4 HOH A 44 205 205 HOH HOH . E 4 HOH A 45 207 207 HOH HOH . E 4 HOH A 46 210 210 HOH HOH . E 4 HOH A 47 211 211 HOH HOH . E 4 HOH A 48 213 213 HOH HOH . E 4 HOH A 49 215 215 HOH HOH . E 4 HOH A 50 216 216 HOH HOH . E 4 HOH A 51 217 217 HOH HOH . E 4 HOH A 52 218 218 HOH HOH . E 4 HOH A 53 219 219 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 . . . D 3 35.717 9.365 16.34 1 15 ? CHA HEM 154 A 1 HETATM 2 C CHB HEM . . . D 3 32.499 12.908 15.576 1 14 ? CHB HEM 154 A 1 HETATM 3 C CHC HEM . . . D 3 29.28 9.679 13.995 1 13 ? CHC HEM 154 A 1 HETATM 4 C CHD HEM . . . D 3 32.363 6.156 15.053 1 14 ? CHD HEM 154 A 1 HETATM 5 C C1A HEM . . . D 3 35.134 10.658 16.215 1 14 ? C1A HEM 154 A 1 HETATM 6 C C2A HEM . . . D 3 35.753 11.902 16.535 1 14 ? C2A HEM 154 A 1 HETATM 7 C C3A HEM . . . D 3 34.853 12.881 16.361 1 13 ? C3A HEM 154 A 1 HETATM 8 C C4A HEM . . . D 3 33.618 12.237 15.919 1 13 ? C4A HEM 154 A 1 HETATM 9 C CMA HEM . . . D 3 35.016 14.39 16.496 1 11 ? CMA HEM 154 A 1 HETATM 10 C CAA HEM . . . D 3 37.226 12.117 16.97 1 16 ? CAA HEM 154 A 1 HETATM 11 C CBA HEM . . . D 3 38.14 12.621 15.805 1 16 ? CBA HEM 154 A 1 HETATM 12 C CGA HEM . . . D 3 38.13 11.642 14.595 1 17 ? CGA HEM 154 A 1 HETATM 13 O O1A HEM . . . D 3 38.517 10.466 14.831 1 18 ? O1A HEM 154 A 1 HETATM 14 O O2A HEM . . . D 3 37.634 12.062 13.536 1 18 ? O2A HEM 154 A 1 HETATM 15 C C1B HEM . . . D 3 31.334 12.361 15.025 1 14 ? C1B HEM 154 A 1 HETATM 16 C C2B HEM . . . D 3 30.179 13.105 14.646 1 13 ? C2B HEM 154 A 1 HETATM 17 C C3B HEM . . . D 3 29.262 12.205 14.23 1 13 ? C3B HEM 154 A 1 HETATM 18 C C4B HEM . . . D 3 29.886 10.892 14.318 1 11 ? C4B HEM 154 A 1 HETATM 19 C CMB HEM . . . D 3 30.023 14.625 14.786 1 13 ? CMB HEM 154 A 1 HETATM 20 C CAB HEM . . . D 3 27.841 12.46 13.664 1 13 ? CAB HEM 154 A 1 HETATM 21 C CBB HEM . . . D 3 26.935 13.435 14.39 1 15 ? CBB HEM 154 A 1 HETATM 22 C C1C HEM . . . D 3 29.78 8.408 14.229 1 15 ? C1C HEM 154 A 1 HETATM 23 C C2C HEM . . . D 3 29.047 7.126 14.097 1 17 ? C2C HEM 154 A 1 HETATM 24 C C3C HEM . . . D 3 29.924 6.147 14.367 1 16 ? C3C HEM 154 A 1 HETATM 25 C C4C HEM . . . D 3 31.196 6.807 14.719 1 16 ? C4C HEM 154 A 1 HETATM 26 C CMC HEM . . . D 3 27.567 7.05 13.641 1 17 ? CMC HEM 154 A 1 HETATM 27 C CAC HEM . . . D 3 29.808 4.626 14.406 1 16 ? CAC HEM 154 A 1 HETATM 28 C CBC HEM . . . D 3 28.605 3.808 14.339 1 18 ? CBC HEM 154 A 1 HETATM 29 C C1D HEM . . . D 3 33.503 6.7 15.518 1 15 ? C1D HEM 154 A 1 HETATM 30 C C2D HEM . . . D 3 34.668 5.95 16.028 1 16 ? C2D HEM 154 A 1 HETATM 31 C C3D HEM . . . D 3 35.593 6.843 16.335 1 15 ? C3D HEM 154 A 1 HETATM 32 C C4D HEM . . . D 3 35.029 8.152 16.155 1 13 ? C4D HEM 154 A 1 HETATM 33 C CMD HEM . . . D 3 34.697 4.421 16.147 1 15 ? CMD HEM 154 A 1 HETATM 34 C CAD HEM . . . D 3 36.95 6.586 17.099 1 17 ? CAD HEM 154 A 1 HETATM 35 C CBD HEM . . . D 3 36.647 6.504 18.575 1 18 ? CBD HEM 154 A 1 HETATM 36 C CGD HEM . . . D 3 37.489 6.421 19.755 1 23 ? CGD HEM 154 A 1 HETATM 37 O O1D HEM . . . D 3 36.947 6.108 20.857 1 29 ? O1D HEM 154 A 1 HETATM 38 O O2D HEM . . . D 3 38.7 6.628 19.612 1 24 ? O2D HEM 154 A 1 HETATM 39 N NA HEM . . . D 3 33.817 10.867 15.827 1 13 ? NA HEM 154 A 1 HETATM 40 N NB HEM . . . D 3 31.124 11.002 14.811 1 13 ? NB HEM 154 A 1 HETATM 41 N NC HEM . . . D 3 31.063 8.168 14.6 1 14 ? NC HEM 154 A 1 HETATM 42 N ND HEM . . . D 3 33.762 8.034 15.576 1 14 ? ND HEM 154 A 1 HETATM 43 FE FE HEM . . . D 3 32.475 9.534 15.18 1 15 ? FE HEM 154 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #