data_9ESB # _model_server_result.job_id vRkOVNtKAcx1Qrk5NHjsDg _model_server_result.datetime_utc '2025-03-10 03:35:20' _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 9esb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 9ESB # _exptl.entry_id 9ESB _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 2 _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 9ESB _cell.length_a 84.245 _cell.length_b 92.135 _cell.length_c 132.329 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9ESB _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C 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 disulf ? disulf1 A SG CYS 323 A CYS 308 1_555 B SG CYS 323 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A NE2 HIS 361 A HIS 346 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc2 C FE HEM . A HEM 501 1_555 D N4 A1H6T . A A1H6T 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 B NE2 HIS 361 B HIS 346 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc4 E FE HEM . B HEM 501 1_555 F N4 A1H6T . B A1H6T 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? # _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 167 n n CHA C4D HEM doub 168 n n CHA HHA HEM sing 169 n n CHB C4A HEM sing 170 n n CHB C1B HEM doub 171 n n CHB HHB HEM sing 172 n n CHC C4B HEM sing 173 n n CHC C1C HEM doub 174 n n CHC HHC HEM sing 175 n n CHD C4C HEM doub 176 n n CHD C1D HEM sing 177 n n CHD HHD HEM sing 178 n n C1A C2A HEM doub 179 n y C1A NA HEM sing 180 n y C2A C3A HEM sing 181 n y C2A CAA HEM sing 182 n n C3A C4A HEM doub 183 n y C3A CMA HEM sing 184 n n C4A NA HEM sing 185 n y CMA HMA HEM sing 186 n n CMA HMAA HEM sing 187 n n CMA HMAB HEM sing 188 n n CAA CBA HEM sing 189 n n CAA HAA HEM sing 190 n n CAA HAAA HEM sing 191 n n CBA CGA HEM sing 192 n n CBA HBA HEM sing 193 n n CBA HBAA HEM sing 194 n n CGA O1A HEM doub 195 n n CGA O2A HEM sing 196 n n C1B C2B HEM sing 197 n n C1B NB HEM sing 198 n n C2B C3B HEM doub 199 n n C2B CMB HEM sing 200 n n C3B C4B HEM sing 201 n n C3B CAB HEM sing 202 n n C4B NB HEM doub 203 n n CMB HMB HEM sing 204 n n CMB HMBA HEM sing 205 n n CMB HMBB HEM sing 206 n n CAB CBB HEM doub 207 n n CAB HAB HEM sing 208 n n CBB HBB HEM sing 209 n n CBB HBBA HEM sing 210 n n C1C C2C HEM sing 211 n y C1C NC HEM sing 212 n y C2C C3C HEM doub 213 n y C2C CMC HEM sing 214 n n C3C C4C HEM sing 215 n y C3C CAC HEM sing 216 n n C4C NC HEM sing 217 n y CMC HMC HEM sing 218 n n CMC HMCA HEM sing 219 n n CMC HMCB HEM sing 220 n n CAC CBC HEM doub 221 n n CAC HAC HEM sing 222 n n CBC HBC HEM sing 223 n n CBC HBCA HEM sing 224 n n C1D C2D HEM sing 225 n n C1D ND HEM doub 226 n n C2D C3D HEM doub 227 n n C2D CMD HEM sing 228 n n C3D C4D HEM sing 229 n n C3D CAD HEM sing 230 n n C4D ND HEM sing 231 n n CMD HMD HEM sing 232 n n CMD HMDA HEM sing 233 n n CMD HMDB HEM sing 234 n n CAD CBD HEM sing 235 n n CAD HAD HEM sing 236 n n CAD HADA HEM sing 237 n n CBD CGD HEM sing 238 n n CBD HBD HEM sing 239 n n CBD HBDA HEM sing 240 n n CGD O1D HEM doub 241 n n CGD O2D HEM sing 242 n n O2A H2A HEM sing 243 n n O2D H2D HEM sing 244 n n FE NA HEM sing 245 n n FE NB HEM sing 246 n n FE NC HEM sing 247 n n FE ND HEM sing 248 n n # _atom_sites.entry_id 9ESB _atom_sites.fract_transf_matrix[1][1] 0.01187 _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] 0.010854 _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] 0.007557 _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 C 2 HEM A 1 501 501 HEM HEM . D 3 A1H6T A 1 502 1 A1H6T LIG . E 2 HEM B 1 501 501 HEM HEM . F 3 A1H6T B 1 502 2 A1H6T LIG . G 4 HOH A 1 601 3 HOH HOH . G 4 HOH A 2 602 26 HOH HOH . G 4 HOH A 3 603 23 HOH HOH . G 4 HOH A 4 604 80 HOH HOH . G 4 HOH A 5 605 17 HOH HOH . G 4 HOH A 6 606 4 HOH HOH . G 4 HOH A 7 607 25 HOH HOH . G 4 HOH A 8 608 9 HOH HOH . G 4 HOH A 9 609 29 HOH HOH . G 4 HOH A 10 610 41 HOH HOH . G 4 HOH A 11 611 69 HOH HOH . G 4 HOH A 12 612 8 HOH HOH . G 4 HOH A 13 613 42 HOH HOH . G 4 HOH A 14 614 36 HOH HOH . G 4 HOH A 15 615 74 HOH HOH . G 4 HOH A 16 616 43 HOH HOH . G 4 HOH A 17 617 1 HOH HOH . G 4 HOH A 18 618 18 HOH HOH . G 4 HOH A 19 619 54 HOH HOH . G 4 HOH A 20 620 86 HOH HOH . G 4 HOH A 21 621 11 HOH HOH . G 4 HOH A 22 622 46 HOH HOH . G 4 HOH A 23 623 38 HOH HOH . G 4 HOH A 24 624 5 HOH HOH . G 4 HOH A 25 625 55 HOH HOH . G 4 HOH A 26 626 24 HOH HOH . G 4 HOH A 27 627 91 HOH HOH . G 4 HOH A 28 628 47 HOH HOH . G 4 HOH A 29 629 7 HOH HOH . G 4 HOH A 30 630 90 HOH HOH . G 4 HOH A 31 631 70 HOH HOH . G 4 HOH A 32 632 68 HOH HOH . G 4 HOH A 33 633 20 HOH HOH . G 4 HOH A 34 634 56 HOH HOH . G 4 HOH A 35 635 53 HOH HOH . G 4 HOH A 36 636 28 HOH HOH . G 4 HOH A 37 637 27 HOH HOH . G 4 HOH A 38 638 76 HOH HOH . G 4 HOH A 39 639 34 HOH HOH . G 4 HOH A 40 640 66 HOH HOH . G 4 HOH A 41 641 60 HOH HOH . G 4 HOH A 42 642 50 HOH HOH . G 4 HOH A 43 643 92 HOH HOH . H 4 HOH B 1 601 75 HOH HOH . H 4 HOH B 2 602 10 HOH HOH . H 4 HOH B 3 603 33 HOH HOH . H 4 HOH B 4 604 21 HOH HOH . H 4 HOH B 5 605 15 HOH HOH . H 4 HOH B 6 606 13 HOH HOH . H 4 HOH B 7 607 82 HOH HOH . H 4 HOH B 8 608 58 HOH HOH . H 4 HOH B 9 609 30 HOH HOH . H 4 HOH B 10 610 89 HOH HOH . H 4 HOH B 11 611 52 HOH HOH . H 4 HOH B 12 612 2 HOH HOH . H 4 HOH B 13 613 48 HOH HOH . H 4 HOH B 14 614 22 HOH HOH . H 4 HOH B 15 615 61 HOH HOH . H 4 HOH B 16 616 71 HOH HOH . H 4 HOH B 17 617 67 HOH HOH . H 4 HOH B 18 618 45 HOH HOH . H 4 HOH B 19 619 14 HOH HOH . H 4 HOH B 20 620 37 HOH HOH . H 4 HOH B 21 621 39 HOH HOH . H 4 HOH B 22 622 62 HOH HOH . H 4 HOH B 23 623 84 HOH HOH . H 4 HOH B 24 624 31 HOH HOH . H 4 HOH B 25 625 63 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 . . . E 2 20.934 3.337 -20.277 1 37.29 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . E 2 23.014 7.463 -21.735 1 38.11 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . E 2 23.809 8.779 -17.149 1 36.55 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . E 2 21.963 4.519 -15.705 1 36.26 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . E 2 21.462 4.358 -21.11 1 37.9 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . E 2 21.434 4.343 -22.564 1 38.32 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . E 2 22.05 5.507 -22.98 1 38.15 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . E 2 22.423 6.223 -21.775 1 38.11 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . E 2 22.383 5.936 -24.376 1 37.96 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . E 2 20.86 3.262 -23.441 1 38.96 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . E 2 21.651 1.949 -23.398 1 40.03 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . E 2 22.947 2.003 -24.157 1 41.19 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . E 2 23.072 2.603 -25.21 1 42.23 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . E 2 23.931 1.369 -23.578 1 41.06 ? O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . E 2 23.33 8.243 -20.618 1 37.95 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . E 2 23.901 9.575 -20.691 1 38.17 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . E 2 24.152 9.93 -19.378 1 38.23 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . E 2 23.711 8.85 -18.532 1 37.51 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . E 2 24.075 10.373 -21.95 1 38.1 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . E 2 24.776 11.169 -18.906 1 38.46 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . E 2 25.82 11.805 -19.391 1 38.5 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . E 2 23.429 7.679 -16.324 1 36.05 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . E 2 23.695 7.585 -14.898 1 35.91 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . E 2 23.217 6.351 -14.515 1 36.06 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . E 2 22.648 5.73 -15.681 1 36.27 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . E 2 24.347 8.645 -14.06 1 35.51 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . E 2 23.313 5.753 -13.178 1 35.88 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . E 2 23.827 4.557 -12.81 1 35.63 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . E 2 21.393 3.872 -16.82 1 36.2 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . E 2 20.66 2.619 -16.762 1 36.17 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . E 2 20.374 2.278 -18.068 1 36.67 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . E 2 20.944 3.325 -18.899 1 36.87 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . E 2 20.328 1.861 -15.513 1 35.79 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . E 2 19.651 1.044 -18.533 1 36.97 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . E 2 18.199 1.304 -18.933 1 37.33 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . E 2 17.269 1.556 -17.778 1 37.68 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . E 2 16.499 2.502 -17.734 1 37.85 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . E 2 17.31 0.629 -16.855 1 37.76 ? O2D HEM 501 B 1 HETATM 39 N NA HEM . . . E 2 22.063 5.493 -20.663 1 37.87 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . E 2 23.198 7.834 -19.332 1 37.7 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . E 2 22.805 6.561 -16.776 1 36.26 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . E 2 21.545 4.287 -18.1 1 36.85 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . E 2 22.445 6.021 -18.728 1 37.33 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #