data_9ESD # _model_server_result.job_id lWqG5WVwSLL6Mdp7jS8P0w _model_server_result.datetime_utc '2025-06-25 01:25:30' _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 9esd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 9ESD # _exptl.entry_id 9ESD _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 9ESD _cell.length_a 143.736 _cell.length_b 143.736 _cell.length_c 141.218 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9ESD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J,K,L,M,N,O,P _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 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 NE2 HIS 290 A HIS 312 1_555 E FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 E FE HEM . A HEM 401 1_555 F NAP 5PK . A 5PK 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 B NE2 HIS 290 B HIS 312 1_555 G FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc4 G FE HEM . B HEM 401 1_555 H NAP 5PK . B 5PK 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc5 C NE2 HIS 290 C HIS 312 1_555 I FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc6 I FE HEM . C HEM 401 1_555 J NAP 5PK . C 5PK 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc7 D NE2 HIS 290 D HIS 312 1_555 K FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc8 K FE HEM . D HEM 401 1_555 L NAP 5PK . D 5PK 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? # _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 175 n n CHA C4D HEM doub 176 n n CHA HHA HEM sing 177 n n CHB C4A HEM sing 178 n n CHB C1B HEM doub 179 n n CHB HHB HEM sing 180 n n CHC C4B HEM sing 181 n n CHC C1C HEM doub 182 n n CHC HHC HEM sing 183 n n CHD C4C HEM doub 184 n n CHD C1D HEM sing 185 n n CHD HHD HEM sing 186 n n C1A C2A HEM doub 187 n y C1A NA HEM sing 188 n y C2A C3A HEM sing 189 n y C2A CAA HEM sing 190 n n C3A C4A HEM doub 191 n y C3A CMA HEM sing 192 n n C4A NA HEM sing 193 n y CMA HMA HEM sing 194 n n CMA HMAA HEM sing 195 n n CMA HMAB HEM sing 196 n n CAA CBA HEM sing 197 n n CAA HAA HEM sing 198 n n CAA HAAA HEM sing 199 n n CBA CGA HEM sing 200 n n CBA HBA HEM sing 201 n n CBA HBAA HEM sing 202 n n CGA O1A HEM doub 203 n n CGA O2A HEM sing 204 n n C1B C2B HEM sing 205 n n C1B NB HEM sing 206 n n C2B C3B HEM doub 207 n n C2B CMB HEM sing 208 n n C3B C4B HEM sing 209 n n C3B CAB HEM sing 210 n n C4B NB HEM doub 211 n n CMB HMB HEM sing 212 n n CMB HMBA HEM sing 213 n n CMB HMBB HEM sing 214 n n CAB CBB HEM doub 215 n n CAB HAB HEM sing 216 n n CBB HBB HEM sing 217 n n CBB HBBA HEM sing 218 n n C1C C2C HEM sing 219 n y C1C NC HEM sing 220 n y C2C C3C HEM doub 221 n y C2C CMC HEM sing 222 n n C3C C4C HEM sing 223 n y C3C CAC HEM sing 224 n n C4C NC HEM sing 225 n y CMC HMC HEM sing 226 n n CMC HMCA HEM sing 227 n n CMC HMCB HEM sing 228 n n CAC CBC HEM doub 229 n n CAC HAC HEM sing 230 n n CBC HBC HEM sing 231 n n CBC HBCA HEM sing 232 n n C1D C2D HEM sing 233 n n C1D ND HEM doub 234 n n C2D C3D HEM doub 235 n n C2D CMD HEM sing 236 n n C3D C4D HEM sing 237 n n C3D CAD HEM sing 238 n n C4D ND HEM sing 239 n n CMD HMD HEM sing 240 n n CMD HMDA HEM sing 241 n n CMD HMDB HEM sing 242 n n CAD CBD HEM sing 243 n n CAD HAD HEM sing 244 n n CAD HADA HEM sing 245 n n CBD CGD HEM sing 246 n n CBD HBD HEM sing 247 n n CBD HBDA HEM sing 248 n n CGD O1D HEM doub 249 n n CGD O2D HEM sing 250 n n O2A H2A HEM sing 251 n n O2D H2D HEM sing 252 n n FE NA HEM sing 253 n n FE NB HEM sing 254 n n FE NC HEM sing 255 n n FE ND HEM sing 256 n n # _atom_sites.entry_id 9ESD _atom_sites.fract_transf_matrix[1][1] 0.006957 _atom_sites.fract_transf_matrix[1][2] 0.004017 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008033 _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] 0.007081 _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 1 401 401 HEM HEM . F 3 5PK A 1 402 410 5PK DRG . G 2 HEM B 1 401 401 HEM HEM . H 3 5PK B 1 402 410 5PK DRG . I 2 HEM C 1 401 401 HEM HEM . J 3 5PK C 1 402 410 5PK DRG . K 2 HEM D 1 401 401 HEM HEM . L 3 5PK D 1 402 410 5PK DRG . M 4 HOH A 1 501 28 HOH HOH . M 4 HOH A 2 502 24 HOH HOH . M 4 HOH A 3 503 14 HOH HOH . M 4 HOH A 4 504 32 HOH HOH . M 4 HOH A 5 505 7 HOH HOH . M 4 HOH A 6 506 42 HOH HOH . M 4 HOH A 7 507 30 HOH HOH . M 4 HOH A 8 508 21 HOH HOH . M 4 HOH A 9 509 36 HOH HOH . M 4 HOH A 10 510 63 HOH HOH . M 4 HOH A 11 511 4 HOH HOH . M 4 HOH A 12 512 5 HOH HOH . N 4 HOH B 1 501 16 HOH HOH . N 4 HOH B 2 502 51 HOH HOH . N 4 HOH B 3 503 52 HOH HOH . N 4 HOH B 4 504 37 HOH HOH . N 4 HOH B 5 505 15 HOH HOH . N 4 HOH B 6 506 2 HOH HOH . N 4 HOH B 7 507 34 HOH HOH . N 4 HOH B 8 508 27 HOH HOH . N 4 HOH B 9 509 55 HOH HOH . N 4 HOH B 10 510 39 HOH HOH . N 4 HOH B 11 511 3 HOH HOH . N 4 HOH B 12 512 13 HOH HOH . N 4 HOH B 13 513 9 HOH HOH . O 4 HOH C 1 501 58 HOH HOH . O 4 HOH C 2 502 38 HOH HOH . O 4 HOH C 3 503 23 HOH HOH . O 4 HOH C 4 504 59 HOH HOH . O 4 HOH C 5 505 20 HOH HOH . O 4 HOH C 6 506 17 HOH HOH . O 4 HOH C 7 507 50 HOH HOH . O 4 HOH C 8 508 62 HOH HOH . O 4 HOH C 9 509 26 HOH HOH . O 4 HOH C 10 510 49 HOH HOH . O 4 HOH C 11 511 60 HOH HOH . O 4 HOH C 12 512 54 HOH HOH . O 4 HOH C 13 513 25 HOH HOH . O 4 HOH C 14 514 41 HOH HOH . O 4 HOH C 15 515 18 HOH HOH . O 4 HOH C 16 516 8 HOH HOH . O 4 HOH C 17 517 11 HOH HOH . P 4 HOH D 1 501 56 HOH HOH . P 4 HOH D 2 502 22 HOH HOH . P 4 HOH D 3 503 43 HOH HOH . P 4 HOH D 4 504 57 HOH HOH . P 4 HOH D 5 505 35 HOH HOH . P 4 HOH D 6 506 29 HOH HOH . P 4 HOH D 7 507 33 HOH HOH . P 4 HOH D 8 508 61 HOH HOH . P 4 HOH D 9 509 40 HOH HOH . P 4 HOH D 10 510 53 HOH HOH . P 4 HOH D 11 511 31 HOH HOH . P 4 HOH D 12 512 6 HOH HOH . P 4 HOH D 13 513 1 HOH HOH . P 4 HOH D 14 514 10 HOH HOH . P 4 HOH D 15 515 44 HOH HOH . P 4 HOH D 16 516 12 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 . . . G 2 -54.398 16.936 51.117 1 44.58 ? CHA HEM 401 B 1 HETATM 2 C CHB HEM . . . G 2 -49.775 15.797 50.095 1 44.34 ? CHB HEM 401 B 1 HETATM 3 C CHC HEM . . . G 2 -50.918 15.301 45.394 1 43.06 ? CHC HEM 401 B 1 HETATM 4 C CHD HEM . . . G 2 -55.314 17.068 46.351 1 42.97 ? CHD HEM 401 B 1 HETATM 5 C C1A HEM . . . G 2 -53.018 16.633 51.272 1 45.45 ? C1A HEM 401 B 1 HETATM 6 C C2A HEM . . . G 2 -52.315 16.595 52.545 1 46.55 ? C2A HEM 401 B 1 HETATM 7 C C3A HEM . . . G 2 -50.998 16.281 52.262 1 45.33 ? C3A HEM 401 B 1 HETATM 8 C C4A HEM . . . G 2 -50.915 16.131 50.818 1 44.97 ? C4A HEM 401 B 1 HETATM 9 C CMA HEM . . . G 2 -49.86 16.095 53.221 1 45.02 ? CMA HEM 401 B 1 HETATM 10 C CAA HEM . . . G 2 -52.904 16.855 53.904 1 48.67 ? CAA HEM 401 B 1 HETATM 11 C CBA HEM . . . G 2 -52.654 18.276 54.385 1 51.01 ? CBA HEM 401 B 1 HETATM 12 C CGA HEM . . . G 2 -52.996 18.471 55.834 1 52.91 ? CGA HEM 401 B 1 HETATM 13 O O1A HEM . . . G 2 -52.153 18.535 56.713 1 53.44 ? O1A HEM 401 B 1 HETATM 14 O O2A HEM . . . G 2 -54.294 18.552 56.056 1 53.69 ? O2A HEM 401 B 1 HETATM 15 C C1B HEM . . . G 2 -49.664 15.572 48.691 1 43.79 ? C1B HEM 401 B 1 HETATM 16 C C2B HEM . . . G 2 -48.438 15.193 48.015 1 43.26 ? C2B HEM 401 B 1 HETATM 17 C C3B HEM . . . G 2 -48.786 15.035 46.684 1 43.91 ? C3B HEM 401 B 1 HETATM 18 C C4B HEM . . . G 2 -50.186 15.317 46.569 1 43.55 ? C4B HEM 401 B 1 HETATM 19 C CMB HEM . . . G 2 -47.108 15.004 48.678 1 42.86 ? CMB HEM 401 B 1 HETATM 20 C CAB HEM . . . G 2 -47.946 14.633 45.549 1 44.54 ? CAB HEM 401 B 1 HETATM 21 C CBB HEM . . . G 2 -46.677 14.92 45.268 1 44.91 ? CBB HEM 401 B 1 HETATM 22 C C1C HEM . . . G 2 -52.268 15.684 45.235 1 42.77 ? C1C HEM 401 B 1 HETATM 23 C C2C HEM . . . G 2 -52.973 15.716 43.967 1 42.55 ? C2C HEM 401 B 1 HETATM 24 C C3C HEM . . . G 2 -54.207 16.269 44.259 1 42.61 ? C3C HEM 401 B 1 HETATM 25 C C4C HEM . . . G 2 -54.247 16.531 45.661 1 42.75 ? C4C HEM 401 B 1 HETATM 26 C CMC HEM . . . G 2 -52.435 15.213 42.66 1 42.24 ? CMC HEM 401 B 1 HETATM 27 C CAC HEM . . . G 2 -55.298 16.574 43.329 1 42.12 ? CAC HEM 401 B 1 HETATM 28 C CBC HEM . . . G 2 -56.004 17.68 43.216 1 41.81 ? CBC HEM 401 B 1 HETATM 29 C C1D HEM . . . G 2 -55.465 17.19 47.751 1 43.37 ? C1D HEM 401 B 1 HETATM 30 C C2D HEM . . . G 2 -56.724 17.475 48.405 1 43.74 ? C2D HEM 401 B 1 HETATM 31 C C3D HEM . . . G 2 -56.493 17.362 49.754 1 43.71 ? C3D HEM 401 B 1 HETATM 32 C C4D HEM . . . G 2 -55.078 17.055 49.905 1 43.89 ? C4D HEM 401 B 1 HETATM 33 C CMD HEM . . . G 2 -57.994 17.865 47.708 1 43.94 ? CMD HEM 401 B 1 HETATM 34 C CAD HEM . . . G 2 -57.547 17.447 50.822 1 43.52 ? CAD HEM 401 B 1 HETATM 35 C CBD HEM . . . G 2 -58.067 16.072 51.223 1 43.66 ? CBD HEM 401 B 1 HETATM 36 C CGD HEM . . . G 2 -59.203 16.078 52.208 1 43.8 ? CGD HEM 401 B 1 HETATM 37 O O1D HEM . . . G 2 -59.904 15.103 52.398 1 43.03 ? O1D HEM 401 B 1 HETATM 38 O O2D HEM . . . G 2 -59.358 17.204 52.876 1 44.64 ? O2D HEM 401 B 1 HETATM 39 N NA HEM . . . G 2 -52.162 16.349 50.25 1 44.95 ? NA HEM 401 B 1 HETATM 40 N NB HEM . . . G 2 -50.7 15.643 47.817 1 43.53 ? NB HEM 401 B 1 HETATM 41 N NC HEM . . . G 2 -53.049 16.155 46.24 1 43.04 ? NC HEM 401 B 1 HETATM 42 N ND HEM . . . G 2 -54.486 16.95 48.661 1 43.44 ? ND HEM 401 B 1 HETATM 43 FE FE HEM . . . G 2 -52.614 16.235 48.25 1 43.22 ? FE HEM 401 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #