data_3RGK # _model_server_result.job_id QtC8-ZwgTN7n2E5qoQlSJQ _model_server_result.datetime_utc '2024-11-23 16:42:52' _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 3rgk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":154}' # _entry.id 3RGK # _exptl.entry_id 3RGK _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 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 120 _cell.entry_id 3RGK _cell.length_a 86.2 _cell.length_b 86.2 _cell.length_c 35.66 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 NE2 HIS 93 A HIS 93 1_555 B FE HEM . A HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 B FE HEM . A HEM 154 1_555 F O HOH . A HOH 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? # _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 3RGK _atom_sites.fract_transf_matrix[1][1] 0.011601 _atom_sites.fract_transf_matrix[1][2] 0.006698 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013396 _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] 0.028043 _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 HEM A 1 154 154 HEM HEM . C 3 SO4 A 1 300 300 SO4 SO4 . D 3 SO4 A 1 301 301 SO4 SO4 . E 3 SO4 A 1 302 302 SO4 SO4 . F 4 HOH A 1 200 200 HOH HOH . F 4 HOH A 2 201 201 HOH HOH . F 4 HOH A 3 202 202 HOH HOH . F 4 HOH A 4 203 203 HOH HOH . F 4 HOH A 5 204 204 HOH HOH . F 4 HOH A 6 205 205 HOH HOH . F 4 HOH A 7 206 206 HOH HOH . F 4 HOH A 8 207 207 HOH HOH . F 4 HOH A 9 208 208 HOH HOH . F 4 HOH A 10 209 209 HOH HOH . F 4 HOH A 11 210 210 HOH HOH . F 4 HOH A 12 211 211 HOH HOH . F 4 HOH A 13 212 212 HOH HOH . F 4 HOH A 14 213 213 HOH HOH . F 4 HOH A 15 214 214 HOH HOH . F 4 HOH A 16 215 215 HOH HOH . F 4 HOH A 17 216 216 HOH HOH . F 4 HOH A 18 217 217 HOH HOH . F 4 HOH A 19 218 218 HOH HOH . F 4 HOH A 20 219 219 HOH HOH . F 4 HOH A 21 220 220 HOH HOH . F 4 HOH A 22 221 221 HOH HOH . F 4 HOH A 23 222 222 HOH HOH . F 4 HOH A 24 223 223 HOH HOH . F 4 HOH A 25 224 224 HOH HOH . F 4 HOH A 26 225 225 HOH HOH . F 4 HOH A 27 226 226 HOH HOH . F 4 HOH A 28 227 227 HOH HOH . F 4 HOH A 29 228 228 HOH HOH . F 4 HOH A 30 229 229 HOH HOH . F 4 HOH A 31 230 230 HOH HOH . F 4 HOH A 32 231 231 HOH HOH . F 4 HOH A 33 232 232 HOH HOH . F 4 HOH A 34 233 233 HOH HOH . F 4 HOH A 35 234 234 HOH HOH . F 4 HOH A 36 235 235 HOH HOH . F 4 HOH A 37 236 236 HOH HOH . F 4 HOH A 38 237 237 HOH HOH . F 4 HOH A 39 238 238 HOH HOH . F 4 HOH A 40 239 239 HOH HOH . F 4 HOH A 41 240 240 HOH HOH . F 4 HOH A 42 241 241 HOH HOH . F 4 HOH A 43 242 242 HOH HOH . F 4 HOH A 44 243 243 HOH HOH . F 4 HOH A 45 244 244 HOH HOH . F 4 HOH A 46 245 245 HOH HOH . F 4 HOH A 47 246 246 HOH HOH . F 4 HOH A 48 247 247 HOH HOH . F 4 HOH A 49 248 248 HOH HOH . F 4 HOH A 50 249 249 HOH HOH . F 4 HOH A 51 250 250 HOH HOH . F 4 HOH A 52 251 251 HOH HOH . F 4 HOH A 53 252 252 HOH HOH . F 4 HOH A 54 253 253 HOH HOH . F 4 HOH A 55 254 254 HOH HOH . F 4 HOH A 56 255 255 HOH HOH . F 4 HOH A 57 256 256 HOH HOH . F 4 HOH A 58 257 257 HOH HOH . F 4 HOH A 59 258 258 HOH HOH . F 4 HOH A 60 259 259 HOH HOH . F 4 HOH A 61 260 260 HOH HOH . F 4 HOH A 62 261 261 HOH HOH . F 4 HOH A 63 262 262 HOH HOH . F 4 HOH A 64 263 263 HOH HOH . F 4 HOH A 65 264 264 HOH HOH . F 4 HOH A 66 265 265 HOH HOH . F 4 HOH A 67 266 266 HOH HOH . F 4 HOH A 68 267 267 HOH HOH . F 4 HOH A 69 268 268 HOH HOH . F 4 HOH A 70 269 269 HOH HOH . F 4 HOH A 71 270 270 HOH HOH . F 4 HOH A 72 271 271 HOH HOH . F 4 HOH A 73 272 272 HOH HOH . F 4 HOH A 74 273 273 HOH HOH . F 4 HOH A 75 274 274 HOH HOH . F 4 HOH A 76 275 275 HOH HOH . F 4 HOH A 77 276 276 HOH HOH . F 4 HOH A 78 277 277 HOH HOH . F 4 HOH A 79 278 278 HOH HOH . F 4 HOH A 80 279 279 HOH HOH . F 4 HOH A 81 280 280 HOH HOH . F 4 HOH A 82 281 281 HOH HOH . F 4 HOH A 83 282 282 HOH HOH . F 4 HOH A 84 283 283 HOH HOH . F 4 HOH A 85 284 284 HOH HOH . F 4 HOH A 86 285 285 HOH HOH . F 4 HOH A 87 286 286 HOH HOH . F 4 HOH A 88 287 287 HOH HOH . F 4 HOH A 89 288 288 HOH HOH . F 4 HOH A 90 289 289 HOH HOH . F 4 HOH A 91 290 290 HOH HOH . F 4 HOH A 92 291 291 HOH HOH . F 4 HOH A 93 292 292 HOH HOH . F 4 HOH A 94 293 293 HOH HOH . F 4 HOH A 95 294 294 HOH HOH . F 4 HOH A 96 295 295 HOH HOH . F 4 HOH A 97 296 296 HOH HOH . F 4 HOH A 98 297 297 HOH HOH . F 4 HOH A 99 298 298 HOH HOH . F 4 HOH A 100 299 299 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 . . . B 2 -5.248 39.769 -0.25 1 7.67 ? CHA HEM 154 A 1 HETATM 2 C CHB HEM . . . B 2 -3.774 36.79 3.28 1 7.05 ? CHB HEM 154 A 1 HETATM 3 C CHC HEM . . . B 2 -2.879 33.328 0.013 1 7.69 ? CHC HEM 154 A 1 HETATM 4 C CHD HEM . . . B 2 -4.342 36.262 -3.536 1 8 ? CHD HEM 154 A 1 HETATM 5 C C1A HEM . . . B 2 -4.96 39.256 0.996 1 7.6 ? C1A HEM 154 A 1 HETATM 6 C C2A HEM . . . B 2 -5.177 39.925 2.27 1 7.96 ? C2A HEM 154 A 1 HETATM 7 C C3A HEM . . . B 2 -4.762 39.099 3.235 1 7.45 ? C3A HEM 154 A 1 HETATM 8 C C4A HEM . . . B 2 -4.279 37.882 2.615 1 7.44 ? C4A HEM 154 A 1 HETATM 9 C CMA HEM . . . B 2 -4.792 39.352 4.76 1 8.07 ? CMA HEM 154 A 1 HETATM 10 C CAA HEM . . . B 2 -5.789 41.338 2.464 1 7.92 ? CAA HEM 154 A 1 HETATM 11 C CBA HEM . . . B 2 -7.283 41.203 2.814 1 9.61 ? CBA HEM 154 A 1 HETATM 12 C CGA HEM . . . B 2 -8 40.335 1.803 1 10.04 ? CGA HEM 154 A 1 HETATM 13 O O1A HEM . . . B 2 -8.314 39.154 2.116 1 11.6 ? O1A HEM 154 A 1 HETATM 14 O O2A HEM . . . B 2 -8.252 40.816 0.681 1 11.56 ? O2A HEM 154 A 1 HETATM 15 C C1B HEM . . . B 2 -3.405 35.579 2.72 1 7.15 ? C1B HEM 154 A 1 HETATM 16 C C2B HEM . . . B 2 -2.926 34.407 3.429 1 6.66 ? C2B HEM 154 A 1 HETATM 17 C C3B HEM . . . B 2 -2.671 33.453 2.525 1 6.59 ? C3B HEM 154 A 1 HETATM 18 C C4B HEM . . . B 2 -2.989 33.989 1.213 1 6.41 ? C4B HEM 154 A 1 HETATM 19 C CMB HEM . . . B 2 -2.743 34.314 4.962 1 8.15 ? CMB HEM 154 A 1 HETATM 20 C CAB HEM . . . B 2 -2.14 32.029 2.797 1 7.93 ? CAB HEM 154 A 1 HETATM 21 C CBB HEM . . . B 2 -1.071 31.845 3.578 1 9.78 ? CBB HEM 154 A 1 HETATM 22 C C1C HEM . . . B 2 -3.124 33.832 -1.241 1 5.49 ? C1C HEM 154 A 1 HETATM 23 C C2C HEM . . . B 2 -2.772 33.214 -2.517 1 6.19 ? C2C HEM 154 A 1 HETATM 24 C C3C HEM . . . B 2 -3.176 34.035 -3.503 1 7.01 ? C3C HEM 154 A 1 HETATM 25 C C4C HEM . . . B 2 -3.787 35.19 -2.877 1 6.73 ? C4C HEM 154 A 1 HETATM 26 C CMC HEM . . . B 2 -2.069 31.847 -2.657 1 7.31 ? CMC HEM 154 A 1 HETATM 27 C CAC HEM . . . B 2 -3.064 33.891 -5.047 1 9.02 ? CAC HEM 154 A 1 HETATM 28 C CBC HEM . . . B 2 -2.329 32.952 -5.654 1 10.36 ? CBC HEM 154 A 1 HETATM 29 C C1D HEM . . . B 2 -4.658 37.483 -2.99 1 7.3 ? C1D HEM 154 A 1 HETATM 30 C C2D HEM . . . B 2 -4.955 38.67 -3.769 1 7.81 ? C2D HEM 154 A 1 HETATM 31 C C3D HEM . . . B 2 -5.222 39.769 -2.755 1 8.54 ? C3D HEM 154 A 1 HETATM 32 C C4D HEM . . . B 2 -5.066 39.14 -1.458 1 7.59 ? C4D HEM 154 A 1 HETATM 33 C CMD HEM . . . B 2 -4.975 38.808 -5.306 1 9.56 ? CMD HEM 154 A 1 HETATM 34 C CAD HEM . . . B 2 -5.555 41.244 -3.071 1 8.72 ? CAD HEM 154 A 1 HETATM 35 C CBD HEM . . . B 2 -4.185 41.927 -3.157 1 12.68 ? CBD HEM 154 A 1 HETATM 36 C CGD HEM . . . B 2 -4.294 43.389 -3.51 1 13.94 ? CGD HEM 154 A 1 HETATM 37 O O1D HEM . . . B 2 -4.666 43.69 -4.669 1 16.65 ? O1D HEM 154 A 1 HETATM 38 O O2D HEM . . . B 2 -3.996 44.248 -2.643 1 14.3 ? O2D HEM 154 A 1 HETATM 39 N NA HEM . . . B 2 -4.426 38.009 1.247 1 6.7 ? NA HEM 154 A 1 HETATM 40 N NB HEM . . . B 2 -3.428 35.288 1.378 1 6.89 ? NB HEM 154 A 1 HETATM 41 N NC HEM . . . B 2 -3.742 35.033 -1.508 1 6.95 ? NC HEM 154 A 1 HETATM 42 N ND HEM . . . B 2 -4.738 37.8 -1.636 1 7.22 ? ND HEM 154 A 1 HETATM 43 FE FE HEM . . . B 2 -4.147 36.509 -0.127 1 7.8 ? FE HEM 154 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #