data_3PGH # _model_server_result.job_id LZ-jr7unDvpaYi3mH1LQhA _model_server_result.datetime_utc '2024-11-25 06:32:41' _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 3pgh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":682}' # _entry.id 3PGH # _exptl.entry_id 3PGH _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 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 90 _cell.entry_id 3PGH _cell.length_a 179.5 _cell.length_b 133.8 _cell.length_c 117.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PGH _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,N 1 1 C,D,O,P,Q,R,S,T,U,V,W,X 2 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 ? 3 H N N ? 3 M N N ? 3 R N N ? 3 W 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 4 A CYS 36 1_555 A SG CYS 15 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 5 A CYS 37 1_555 A SG CYS 128 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 9 A CYS 41 1_555 A SG CYS 25 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf4 A SG CYS 27 A CYS 59 1_555 A SG CYS 37 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 A SG CYS 538 A CYS 569 1_555 A SG CYS 544 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf6 B SG CYS 4 B CYS 36 1_555 B SG CYS 15 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf7 B SG CYS 5 B CYS 37 1_555 B SG CYS 128 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf8 B SG CYS 9 B CYS 41 1_555 B SG CYS 25 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf9 B SG CYS 27 B CYS 59 1_555 B SG CYS 37 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf10 B SG CYS 538 B CYS 569 1_555 B SG CYS 544 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf11 C SG CYS 4 C CYS 36 1_555 C SG CYS 15 C CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf12 C SG CYS 5 C CYS 37 1_555 C SG CYS 128 C CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf13 C SG CYS 9 C CYS 41 1_555 C SG CYS 25 C CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf14 C SG CYS 27 C CYS 59 1_555 C SG CYS 37 C CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 C SG CYS 538 C CYS 569 1_555 C SG CYS 544 C CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf16 D SG CYS 4 D CYS 36 1_555 D SG CYS 15 D CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf17 D SG CYS 5 D CYS 37 1_555 D SG CYS 128 D CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf18 D SG CYS 9 D CYS 41 1_555 D SG CYS 25 D CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf19 D SG CYS 27 D CYS 59 1_555 D SG CYS 37 D CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf20 D SG CYS 538 D CYS 569 1_555 D SG CYS 544 D CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 36 A ASN 68 1_555 E C1 NAG . A NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 113 A ASN 144 1_555 F C1 NAG . A NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 A ND2 ASN 379 A ASN 410 1_555 G C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale4 B ND2 ASN 36 B ASN 68 1_555 J C1 NAG . B NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 B ND2 ASN 113 B ASN 144 1_555 K C1 NAG . B NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 379 B ASN 410 1_555 L C1 NAG . B NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 C ND2 ASN 36 C ASN 68 1_555 O C1 NAG . C NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 113 C ASN 144 1_555 P C1 NAG . C NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale9 C ND2 ASN 379 C ASN 410 1_555 Q C1 NAG . C NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 D ND2 ASN 36 D ASN 68 1_555 T C1 NAG . D NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale11 D ND2 ASN 113 D ASN 144 1_555 U C1 NAG . D NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D ND2 ASN 379 D ASN 410 1_555 V C1 NAG . D NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? metalc ? metalc1 A NE2 HIS 357 A HIS 388 1_555 H FE HEM . A HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc2 B NE2 HIS 357 B HIS 388 1_555 M FE HEM . B HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 C NE2 HIS 357 C HIS 388 1_555 R FE HEM . C HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc4 D NE2 HIS 357 D HIS 388 1_555 W FE HEM . D HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 161 n n CHA C4D HEM doub 162 n n CHA HHA HEM sing 163 n n CHB C4A HEM sing 164 n n CHB C1B HEM doub 165 n n CHB HHB HEM sing 166 n n CHC C4B HEM sing 167 n n CHC C1C HEM doub 168 n n CHC HHC HEM sing 169 n n CHD C4C HEM doub 170 n n CHD C1D HEM sing 171 n n CHD HHD HEM sing 172 n n C1A C2A HEM doub 173 n y C1A NA HEM sing 174 n y C2A C3A HEM sing 175 n y C2A CAA HEM sing 176 n n C3A C4A HEM doub 177 n y C3A CMA HEM sing 178 n n C4A NA HEM sing 179 n y CMA HMA HEM sing 180 n n CMA HMAA HEM sing 181 n n CMA HMAB HEM sing 182 n n CAA CBA HEM sing 183 n n CAA HAA HEM sing 184 n n CAA HAAA HEM sing 185 n n CBA CGA HEM sing 186 n n CBA HBA HEM sing 187 n n CBA HBAA HEM sing 188 n n CGA O1A HEM doub 189 n n CGA O2A HEM sing 190 n n C1B C2B HEM sing 191 n n C1B NB HEM sing 192 n n C2B C3B HEM doub 193 n n C2B CMB HEM sing 194 n n C3B C4B HEM sing 195 n n C3B CAB HEM sing 196 n n C4B NB HEM doub 197 n n CMB HMB HEM sing 198 n n CMB HMBA HEM sing 199 n n CMB HMBB HEM sing 200 n n CAB CBB HEM doub 201 n n CAB HAB HEM sing 202 n n CBB HBB HEM sing 203 n n CBB HBBA HEM sing 204 n n C1C C2C HEM sing 205 n y C1C NC HEM sing 206 n y C2C C3C HEM doub 207 n y C2C CMC HEM sing 208 n n C3C C4C HEM sing 209 n y C3C CAC HEM sing 210 n n C4C NC HEM sing 211 n y CMC HMC HEM sing 212 n n CMC HMCA HEM sing 213 n n CMC HMCB HEM sing 214 n n CAC CBC HEM doub 215 n n CAC HAC HEM sing 216 n n CBC HBC HEM sing 217 n n CBC HBCA HEM sing 218 n n C1D C2D HEM sing 219 n n C1D ND HEM doub 220 n n C2D C3D HEM doub 221 n n C2D CMD HEM sing 222 n n C3D C4D HEM sing 223 n n C3D CAD HEM sing 224 n n C4D ND HEM sing 225 n n CMD HMD HEM sing 226 n n CMD HMDA HEM sing 227 n n CMD HMDB HEM sing 228 n n CAD CBD HEM sing 229 n n CAD HAD HEM sing 230 n n CAD HADA HEM sing 231 n n CBD CGD HEM sing 232 n n CBD HBD HEM sing 233 n n CBD HBDA HEM sing 234 n n CGD O1D HEM doub 235 n n CGD O2D HEM sing 236 n n O2A H2A HEM sing 237 n n O2D H2D HEM sing 238 n n FE NA HEM sing 239 n n FE NB HEM sing 240 n n FE NC HEM sing 241 n n FE ND HEM sing 242 n n # _atom_sites.entry_id 3PGH _atom_sites.fract_transf_matrix[1][1] 0.005571 _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] 0.007474 _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] 0.00854 _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 NAG A 1 661 661 NAG NAG . F 2 NAG A 1 671 671 NAG NAG . G 2 NAG A 1 681 681 NAG NAG . H 3 HEM A 1 682 601 HEM HEM . I 4 FLP A 1 701 701 FLP FLP . J 2 NAG B 1 661 661 NAG NAG . K 2 NAG B 1 671 671 NAG NAG . L 2 NAG B 1 681 681 NAG NAG . M 3 HEM B 1 682 601 HEM HEM . N 4 FLP B 1 701 701 FLP FLP . O 2 NAG C 1 661 661 NAG NAG . P 2 NAG C 1 671 671 NAG NAG . Q 2 NAG C 1 681 681 NAG NAG . R 3 HEM C 1 682 601 HEM HEM . S 4 FLP C 1 701 701 FLP FLP . T 2 NAG D 1 661 661 NAG NAG . U 2 NAG D 1 671 671 NAG NAG . V 2 NAG D 1 681 681 NAG NAG . W 3 HEM D 1 682 601 HEM HEM . X 4 FLP D 1 701 701 FLP FLP . # 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 . . . R 3 59.919 31.779 57.633 1 8.68 ? CHA HEM 682 C 1 HETATM 2 C CHB HEM . . . R 3 63.07 28.171 58.025 1 11.04 ? CHB HEM 682 C 1 HETATM 3 C CHC HEM . . . R 3 63.602 29.188 62.643 1 12.74 ? CHC HEM 682 C 1 HETATM 4 C CHD HEM . . . R 3 60.903 33.062 62.156 1 14.34 ? CHD HEM 682 C 1 HETATM 5 C C1A HEM . . . R 3 60.786 30.755 57.308 1 17.2 ? C1A HEM 682 C 1 HETATM 6 C C2A HEM . . . R 3 60.835 30.103 56.01 1 20.78 ? C2A HEM 682 C 1 HETATM 7 C C3A HEM . . . R 3 61.749 29.08 56.128 1 13.71 ? C3A HEM 682 C 1 HETATM 8 C C4A HEM . . . R 3 62.243 29.13 57.48 1 10.89 ? C4A HEM 682 C 1 HETATM 9 C CMA HEM . . . R 3 62.176 28.071 55.066 1 2.47 ? CMA HEM 682 C 1 HETATM 10 C CAA HEM . . . R 3 60.045 30.526 54.763 1 23.11 ? CAA HEM 682 C 1 HETATM 11 C CBA HEM . . . R 3 60.898 31.301 53.752 1 32.24 ? CBA HEM 682 C 1 HETATM 12 C CGA HEM . . . R 3 60.105 31.859 52.578 1 34.68 ? CGA HEM 682 C 1 HETATM 13 O O1A HEM . . . R 3 59.606 33.001 52.691 1 42.31 ? O1A HEM 682 C 1 HETATM 14 O O2A HEM . . . R 3 59.994 31.178 51.537 1 34.36 ? O2A HEM 682 C 1 HETATM 15 C C1B HEM . . . R 3 63.461 28.111 59.34 1 6.56 ? C1B HEM 682 C 1 HETATM 16 C C2B HEM . . . R 3 64.179 27.012 59.931 1 8.55 ? C2B HEM 682 C 1 HETATM 17 C C3B HEM . . . R 3 64.222 27.257 61.269 1 7.23 ? C3B HEM 682 C 1 HETATM 18 C C4B HEM . . . R 3 63.625 28.534 61.44 1 7.56 ? C4B HEM 682 C 1 HETATM 19 C CMB HEM . . . R 3 64.842 25.872 59.167 1 6.5 ? CMB HEM 682 C 1 HETATM 20 C CAB HEM . . . R 3 64.531 26.404 62.321 1 3.53 ? CAB HEM 682 C 1 HETATM 21 C CBB HEM . . . R 3 65.691 25.561 62.326 1 8.33 ? CBB HEM 682 C 1 HETATM 22 C C1C HEM . . . R 3 63.011 30.397 62.876 1 5.98 ? C1C HEM 682 C 1 HETATM 23 C C2C HEM . . . R 3 62.986 31.009 64.16 1 9.68 ? C2C HEM 682 C 1 HETATM 24 C C3C HEM . . . R 3 62.26 32.122 64.029 1 12.36 ? C3C HEM 682 C 1 HETATM 25 C C4C HEM . . . R 3 61.827 32.165 62.65 1 11.82 ? C4C HEM 682 C 1 HETATM 26 C CMC HEM . . . R 3 63.657 30.491 65.423 1 7.79 ? CMC HEM 682 C 1 HETATM 27 C CAC HEM . . . R 3 62.076 33.07 65.011 1 14.44 ? CAC HEM 682 C 1 HETATM 28 C CBC HEM . . . R 3 60.841 33.784 65.164 1 19.68 ? CBC HEM 682 C 1 HETATM 29 C C1D HEM . . . R 3 60.361 33.02 60.892 1 15.88 ? C1D HEM 682 C 1 HETATM 30 C C2D HEM . . . R 3 59.306 33.886 60.453 1 11.27 ? C2D HEM 682 C 1 HETATM 31 C C3D HEM . . . R 3 58.976 33.49 59.207 1 12.29 ? C3D HEM 682 C 1 HETATM 32 C C4D HEM . . . R 3 59.867 32.399 58.863 1 13.1 ? C4D HEM 682 C 1 HETATM 33 C CMD HEM . . . R 3 58.665 34.971 61.28 1 13.72 ? CMD HEM 682 C 1 HETATM 34 C CAD HEM . . . R 3 57.76 33.917 58.408 1 10.05 ? CAD HEM 682 C 1 HETATM 35 C CBD HEM . . . R 3 56.544 33.053 58.641 1 4.69 ? CBD HEM 682 C 1 HETATM 36 C CGD HEM . . . R 3 55.595 33.099 57.487 1 8.6 ? CGD HEM 682 C 1 HETATM 37 O O1D HEM . . . R 3 55.295 34.206 57.01 1 9.36 ? O1D HEM 682 C 1 HETATM 38 O O2D HEM . . . R 3 55.145 32.035 57.043 1 7.05 ? O2D HEM 682 C 1 HETATM 39 N NA HEM . . . R 3 61.68 30.168 58.189 1 11.33 ? NA HEM 682 C 1 HETATM 40 N NB HEM . . . R 3 63.118 29.038 60.273 1 7.63 ? NB HEM 682 C 1 HETATM 41 N NC HEM . . . R 3 62.32 31.106 61.941 1 6.89 ? NC HEM 682 C 1 HETATM 42 N ND HEM . . . R 3 60.699 32.097 59.916 1 15.3 ? ND HEM 682 C 1 HETATM 43 FE FE HEM . . . R 3 62.019 30.654 60.034 1 15.99 ? FE HEM 682 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #