data_3CYR # _model_server_result.job_id CZx3fZTN-O-sGO0d0oG02A _model_server_result.datetime_utc '2025-03-09 06:14:41' _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 3cyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 3CYR # _exptl.entry_id 3CYR _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 120 _cell.entry_id 3CYR _cell.length_a 62.71 _cell.length_b 62.71 _cell.length_c 111.09 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D 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 covale ? covale1 A SG CYS 30 A CYS 30 1_555 B CAB HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale2 A SG CYS 33 A CYS 33 1_555 B CAC HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale3 A SG CYS 46 A CYS 46 1_555 C CAB HEM . A HEM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale4 A SG CYS 51 A CYS 51 1_555 C CAC HEM . A HEM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale5 A SG CYS 79 A CYS 79 1_555 D CAB HEM . A HEM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale6 A SG CYS 82 A CYS 82 1_555 D CAC HEM . A HEM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale7 A SG CYS 100 A CYS 100 1_555 E CAB HEM . A HEM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale8 A SG CYS 105 A CYS 105 1_555 E CAC HEM . A HEM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc1 A NE2 HIS 22 A HIS 22 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 A NE2 HIS 25 A HIS 25 1_555 D FE HEM . A HEM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 A NE2 HIS 34 A HIS 34 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc4 A NE2 HIS 35 A HIS 35 1_555 C FE HEM . A HEM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc5 A NE2 HIS 52 A HIS 52 1_555 C FE HEM . A HEM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc6 A NE2 HIS 69 A HIS 69 1_555 E FE HEM . A HEM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc7 A NE2 HIS 83 A HIS 83 1_555 D FE HEM . A HEM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc8 A NE2 HIS 106 A HIS 106 1_555 E FE HEM . A HEM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _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 103 n n CHA C4D HEM doub 104 n n CHA HHA HEM sing 105 n n CHB C4A HEM sing 106 n n CHB C1B HEM doub 107 n n CHB HHB HEM sing 108 n n CHC C4B HEM sing 109 n n CHC C1C HEM doub 110 n n CHC HHC HEM sing 111 n n CHD C4C HEM doub 112 n n CHD C1D HEM sing 113 n n CHD HHD HEM sing 114 n n C1A C2A HEM doub 115 n y C1A NA HEM sing 116 n y C2A C3A HEM sing 117 n y C2A CAA HEM sing 118 n n C3A C4A HEM doub 119 n y C3A CMA HEM sing 120 n n C4A NA HEM sing 121 n y CMA HMA HEM sing 122 n n CMA HMAA HEM sing 123 n n CMA HMAB HEM sing 124 n n CAA CBA HEM sing 125 n n CAA HAA HEM sing 126 n n CAA HAAA HEM sing 127 n n CBA CGA HEM sing 128 n n CBA HBA HEM sing 129 n n CBA HBAA HEM sing 130 n n CGA O1A HEM doub 131 n n CGA O2A HEM sing 132 n n C1B C2B HEM sing 133 n n C1B NB HEM sing 134 n n C2B C3B HEM doub 135 n n C2B CMB HEM sing 136 n n C3B C4B HEM sing 137 n n C3B CAB HEM sing 138 n n C4B NB HEM doub 139 n n CMB HMB HEM sing 140 n n CMB HMBA HEM sing 141 n n CMB HMBB HEM sing 142 n n CAB CBB HEM doub 143 n n CAB HAB HEM sing 144 n n CBB HBB HEM sing 145 n n CBB HBBA HEM sing 146 n n C1C C2C HEM sing 147 n y C1C NC HEM sing 148 n y C2C C3C HEM doub 149 n y C2C CMC HEM sing 150 n n C3C C4C HEM sing 151 n y C3C CAC HEM sing 152 n n C4C NC HEM sing 153 n y CMC HMC HEM sing 154 n n CMC HMCA HEM sing 155 n n CMC HMCB HEM sing 156 n n CAC CBC HEM doub 157 n n CAC HAC HEM sing 158 n n CBC HBC HEM sing 159 n n CBC HBCA HEM sing 160 n n C1D C2D HEM sing 161 n n C1D ND HEM doub 162 n n C2D C3D HEM doub 163 n n C2D CMD HEM sing 164 n n C3D C4D HEM sing 165 n n C3D CAD HEM sing 166 n n C4D ND HEM sing 167 n n CMD HMD HEM sing 168 n n CMD HMDA HEM sing 169 n n CMD HMDB HEM sing 170 n n CAD CBD HEM sing 171 n n CAD HAD HEM sing 172 n n CAD HADA HEM sing 173 n n CBD CGD HEM sing 174 n n CBD HBD HEM sing 175 n n CBD HBDA HEM sing 176 n n CGD O1D HEM doub 177 n n CGD O2D HEM sing 178 n n O2A H2A HEM sing 179 n n O2D H2D HEM sing 180 n n FE NA HEM sing 181 n n FE NB HEM sing 182 n n FE NC HEM sing 183 n n FE ND HEM sing 184 n n # _atom_sites.entry_id 3CYR _atom_sites.fract_transf_matrix[1][1] 0.015946 _atom_sites.fract_transf_matrix[1][2] 0.009207 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018413 _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] 0.009002 _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 1 201 201 HEM HEM . C 2 HEM A 1 202 202 HEM HEM . D 2 HEM A 1 203 203 HEM HEM . E 2 HEM A 1 204 204 HEM HEM . F 3 HOH A 1 205 205 HOH HOH . F 3 HOH A 2 206 206 HOH HOH . F 3 HOH A 3 207 207 HOH HOH . F 3 HOH A 4 208 208 HOH HOH . F 3 HOH A 5 209 209 HOH HOH . F 3 HOH A 6 210 210 HOH HOH . F 3 HOH A 7 211 211 HOH HOH . F 3 HOH A 8 212 212 HOH HOH . F 3 HOH A 9 213 213 HOH HOH . F 3 HOH A 10 214 214 HOH HOH . F 3 HOH A 11 215 215 HOH HOH . F 3 HOH A 12 216 216 HOH HOH . F 3 HOH A 13 217 217 HOH HOH . F 3 HOH A 14 218 218 HOH HOH . F 3 HOH A 15 219 219 HOH HOH . F 3 HOH A 16 220 220 HOH HOH . F 3 HOH A 17 221 221 HOH HOH . F 3 HOH A 18 222 222 HOH HOH . F 3 HOH A 19 223 223 HOH HOH . F 3 HOH A 20 224 224 HOH HOH . F 3 HOH A 21 225 225 HOH HOH . F 3 HOH A 22 226 226 HOH HOH . F 3 HOH A 23 227 227 HOH HOH . F 3 HOH A 24 228 228 HOH HOH . F 3 HOH A 25 229 229 HOH HOH . F 3 HOH A 26 230 230 HOH HOH . F 3 HOH A 27 231 231 HOH HOH . F 3 HOH A 28 232 232 HOH HOH . F 3 HOH A 29 233 233 HOH HOH . F 3 HOH A 30 234 234 HOH HOH . F 3 HOH A 31 235 235 HOH HOH . F 3 HOH A 32 236 236 HOH HOH . F 3 HOH A 33 237 237 HOH HOH . F 3 HOH A 34 238 238 HOH HOH . F 3 HOH A 35 239 239 HOH HOH . F 3 HOH A 36 240 240 HOH HOH . F 3 HOH A 37 241 241 HOH HOH . F 3 HOH A 38 242 242 HOH HOH . F 3 HOH A 39 243 243 HOH HOH . F 3 HOH A 40 244 244 HOH HOH . F 3 HOH A 41 245 245 HOH HOH . F 3 HOH A 42 246 246 HOH HOH . F 3 HOH A 43 247 247 HOH HOH . F 3 HOH A 44 248 248 HOH HOH . F 3 HOH A 45 249 249 HOH HOH . F 3 HOH A 46 250 250 HOH HOH . F 3 HOH A 47 251 251 HOH HOH . F 3 HOH A 48 252 252 HOH HOH . F 3 HOH A 49 253 253 HOH HOH . F 3 HOH A 50 254 254 HOH HOH . F 3 HOH A 51 255 255 HOH HOH . F 3 HOH A 52 256 256 HOH HOH . F 3 HOH A 53 257 257 HOH HOH . F 3 HOH A 54 258 258 HOH HOH . F 3 HOH A 55 259 259 HOH HOH . F 3 HOH A 56 260 260 HOH HOH . F 3 HOH A 57 261 261 HOH HOH . F 3 HOH A 58 262 262 HOH HOH . F 3 HOH A 59 263 263 HOH HOH . F 3 HOH A 60 264 264 HOH HOH . F 3 HOH A 61 265 265 HOH HOH . F 3 HOH A 62 266 266 HOH HOH . F 3 HOH A 63 267 267 HOH HOH . F 3 HOH A 64 268 268 HOH HOH . F 3 HOH A 65 269 269 HOH HOH . F 3 HOH A 66 270 270 HOH HOH . F 3 HOH A 67 271 271 HOH HOH . F 3 HOH A 68 272 272 HOH HOH . F 3 HOH A 69 273 273 HOH HOH . F 3 HOH A 70 274 274 HOH HOH . F 3 HOH A 71 275 275 HOH HOH . F 3 HOH A 72 276 276 HOH HOH . F 3 HOH A 73 277 277 HOH HOH . F 3 HOH A 74 278 278 HOH HOH . F 3 HOH A 75 279 279 HOH HOH . F 3 HOH A 76 280 280 HOH HOH . F 3 HOH A 77 281 281 HOH HOH . F 3 HOH A 78 282 282 HOH HOH . F 3 HOH A 79 284 284 HOH HOH . F 3 HOH A 80 288 288 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 2 22.762 49.249 33.636 1 11.5 ? CHA HEM 203 A 1 HETATM 2 C CHB HEM . . . D 2 19.823 46.525 36.382 1 10.69 ? CHB HEM 203 A 1 HETATM 3 C CHC HEM . . . D 2 16.087 49.369 35.103 1 9.54 ? CHC HEM 203 A 1 HETATM 4 C CHD HEM . . . D 2 18.962 51.894 32.12 1 10.66 ? CHD HEM 203 A 1 HETATM 5 C C1A HEM . . . D 2 22.293 48.245 34.467 1 11 ? C1A HEM 203 A 1 HETATM 6 C C2A HEM . . . D 2 23.085 47.185 35.057 1 13.55 ? C2A HEM 203 A 1 HETATM 7 C C3A HEM . . . D 2 22.287 46.464 35.843 1 12.26 ? C3A HEM 203 A 1 HETATM 8 C C4A HEM . . . D 2 20.954 47.002 35.733 1 11.96 ? C4A HEM 203 A 1 HETATM 9 C CMA HEM . . . D 2 22.628 45.184 36.642 1 14.91 ? CMA HEM 203 A 1 HETATM 10 C CAA HEM . . . D 2 24.59 46.957 34.681 1 19.03 ? CAA HEM 203 A 1 HETATM 11 C CBA HEM . . . D 2 25.539 47.828 35.546 1 26.37 ? CBA HEM 203 A 1 HETATM 12 C CGA HEM . . . D 2 26.84 47.166 35.913 1 41.71 ? CGA HEM 203 A 1 HETATM 13 O O1A HEM . . . D 2 27.284 46.286 35.134 1 45.13 ? O1A HEM 203 A 1 HETATM 14 O O2A HEM . . . D 2 27.372 47.569 36.993 1 62.95 ? O2A HEM 203 A 1 HETATM 15 C C1B HEM . . . D 2 18.542 47.071 36.269 1 11.37 ? C1B HEM 203 A 1 HETATM 16 C C2B HEM . . . D 2 17.338 46.519 36.872 1 10.59 ? C2B HEM 203 A 1 HETATM 17 C C3B HEM . . . D 2 16.282 47.284 36.549 1 9.84 ? C3B HEM 203 A 1 HETATM 18 C C4B HEM . . . D 2 16.826 48.342 35.679 1 8.95 ? C4B HEM 203 A 1 HETATM 19 C CMB HEM . . . D 2 17.38 45.241 37.751 1 9.85 ? CMB HEM 203 A 1 HETATM 20 C CAB HEM . . . D 2 14.837 47.251 37.044 1 9.38 ? CAB HEM 203 A 1 HETATM 21 C CBB HEM . . . D 2 14.689 47.386 38.468 1 13.2 ? CBB HEM 203 A 1 HETATM 22 C C1C HEM . . . D 2 16.569 50.287 34.179 1 10.72 ? C1C HEM 203 A 1 HETATM 23 C C2C HEM . . . D 2 15.733 51.309 33.52 1 11.93 ? C2C HEM 203 A 1 HETATM 24 C C3C HEM . . . D 2 16.482 51.961 32.633 1 10.19 ? C3C HEM 203 A 1 HETATM 25 C C4C HEM . . . D 2 17.818 51.44 32.773 1 11.13 ? C4C HEM 203 A 1 HETATM 26 C CMC HEM . . . D 2 14.219 51.395 33.784 1 13.88 ? CMC HEM 203 A 1 HETATM 27 C CAC HEM . . . D 2 16.076 53.038 31.588 1 10.53 ? CAC HEM 203 A 1 HETATM 28 C CBC HEM . . . D 2 15.022 53.885 31.935 1 15.45 ? CBC HEM 203 A 1 HETATM 29 C C1D HEM . . . D 2 20.26 51.44 32.319 1 12.49 ? C1D HEM 203 A 1 HETATM 30 C C2D HEM . . . D 2 21.447 51.99 31.726 1 11.17 ? C2D HEM 203 A 1 HETATM 31 C C3D HEM . . . D 2 22.507 51.301 32.175 1 11.91 ? C3D HEM 203 A 1 HETATM 32 C C4D HEM . . . D 2 22.004 50.23 33.028 1 11.81 ? C4D HEM 203 A 1 HETATM 33 C CMD HEM . . . D 2 21.466 53.199 30.745 1 14.37 ? CMD HEM 203 A 1 HETATM 34 C CAD HEM . . . D 2 23.985 51.499 31.766 1 13 ? CAD HEM 203 A 1 HETATM 35 C CBD HEM . . . D 2 24.291 51.058 30.324 1 17.98 ? CBD HEM 203 A 1 HETATM 36 C CGD HEM . . . D 2 25.582 51.612 29.747 1 27.67 ? CGD HEM 203 A 1 HETATM 37 O O1D HEM . . . D 2 26.618 51.299 30.353 1 25.9 ? O1D HEM 203 A 1 HETATM 38 O O2D HEM . . . D 2 25.46 52.306 28.696 1 31.03 ? O2D HEM 203 A 1 HETATM 39 N NA HEM . . . D 2 20.981 48.104 34.867 1 10.09 ? NA HEM 203 A 1 HETATM 40 N NB HEM . . . D 2 18.193 48.183 35.51 1 9.16 ? NB HEM 203 A 1 HETATM 41 N NC HEM . . . D 2 17.839 50.38 33.701 1 11.19 ? NC HEM 203 A 1 HETATM 42 N ND HEM . . . D 2 20.633 50.334 33.098 1 8.66 ? ND HEM 203 A 1 HETATM 43 FE FE HEM . . . D 2 19.421 49.236 34.264 1 10.53 ? FE HEM 203 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #