data_4L3V # _model_server_result.job_id dz4xfyyK-IQb1uZRmjSV0w _model_server_result.datetime_utc '2024-12-01 23:33:31' _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 4l3v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 4L3V # _exptl.entry_id 4L3V _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 3 _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 4L3V _cell.length_a 227.75 _cell.length_b 342.655 _cell.length_c 107.253 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L3V _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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,D,E 1 1,2 B,C,F,G,H,I 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_353 -x-2,y,-z-3/2 -1 0 0 0 1 0 0 0 -1 -455.5 0 -160.8795 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I 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 NZ LYS 118 B LYS 119 1_555 D C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 doub covale ? covale2 B NZ LYS 118 A LYS 119 1_555 F C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 doub covale ? covale3 C NZ LYS 118 C LYS 119 1_555 H C4A PLP . C PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 doub metalc ? metalc1 A SG CYS 51 B CYS 52 1_555 E FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 A NE2 HIS 64 B HIS 65 1_555 E FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 B SG CYS 51 A CYS 52 1_555 G FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc4 B NE2 HIS 64 A HIS 65 1_555 G FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc5 C SG CYS 51 C CYS 52 1_555 I FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 C NE2 HIS 64 C HIS 65 1_555 I FE HEM . C HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 4L3V _atom_sites.fract_transf_matrix[1][1] 0.004391 _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] 0.002918 _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] 0.009324 _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 D 2 PLP B 1 601 1000 PLP PLP . E 3 HEM B 1 602 2000 HEM HEM . F 2 PLP A 1 601 1000 PLP PLP . G 3 HEM A 1 602 2000 HEM HEM . H 2 PLP C 1 601 1000 PLP PLP . I 3 HEM C 1 602 2000 HEM HEM . # 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 3 -217.27 393.544 -110.641 1 34.5 ? CHA HEM 602 B 1 HETATM 2 C CHB HEM . . . E 3 -215.547 398.079 -110.994 1 34.57 ? CHB HEM 602 B 1 HETATM 3 C CHC HEM . . . E 3 -215.106 398.39 -106.185 1 34.3 ? CHC HEM 602 B 1 HETATM 4 C CHD HEM . . . E 3 -216.831 393.919 -105.862 1 34.21 ? CHD HEM 602 B 1 HETATM 5 C C1A HEM . . . E 3 -216.922 394.782 -111.146 1 34.59 ? C1A HEM 602 B 1 HETATM 6 C C2A HEM . . . E 3 -217.121 395.219 -112.509 1 34.73 ? C2A HEM 602 B 1 HETATM 7 C C3A HEM . . . E 3 -216.65 396.467 -112.588 1 34.66 ? C3A HEM 602 B 1 HETATM 8 C C4A HEM . . . E 3 -216.121 396.86 -111.304 1 34.59 ? C4A HEM 602 B 1 HETATM 9 C CMA HEM . . . E 3 -216.622 397.395 -113.797 1 34.67 ? CMA HEM 602 B 1 HETATM 10 C CAA HEM . . . E 3 -217.82 394.358 -113.58 1 34.88 ? CAA HEM 602 B 1 HETATM 11 C CBA HEM . . . E 3 -216.915 393.762 -114.636 1 35.01 ? CBA HEM 602 B 1 HETATM 12 C CGA HEM . . . E 3 -217.83 393.109 -115.645 1 35.11 ? CGA HEM 602 B 1 HETATM 13 O O1A HEM . . . E 3 -218.649 392.25 -115.228 1 35.28 ? O1A HEM 602 B 1 HETATM 14 O O2A HEM . . . E 3 -217.758 393.443 -116.861 1 35.15 ? O2A HEM 602 B 1 HETATM 15 C C1B HEM . . . E 3 -215.269 398.56 -109.732 1 34.55 ? C1B HEM 602 B 1 HETATM 16 C C2B HEM . . . E 3 -214.745 399.879 -109.428 1 34.62 ? C2B HEM 602 B 1 HETATM 17 C C3B HEM . . . E 3 -214.618 399.97 -108.1 1 34.5 ? C3B HEM 602 B 1 HETATM 18 C C4B HEM . . . E 3 -215.067 398.714 -107.526 1 34.41 ? C4B HEM 602 B 1 HETATM 19 C CMB HEM . . . E 3 -214.416 400.946 -110.502 1 34.71 ? CMB HEM 602 B 1 HETATM 20 C CAB HEM . . . E 3 -214.11 401.166 -107.258 1 34.5 ? CAB HEM 602 B 1 HETATM 21 C CBB HEM . . . E 3 -213.793 402.375 -107.74 1 34.51 ? CBB HEM 602 B 1 HETATM 22 C C1C HEM . . . E 3 -215.527 397.192 -105.697 1 34.22 ? C1C HEM 602 B 1 HETATM 23 C C2C HEM . . . E 3 -215.478 396.816 -104.301 1 34.11 ? C2C HEM 602 B 1 HETATM 24 C C3C HEM . . . E 3 -215.975 395.582 -104.205 1 34.05 ? C3C HEM 602 B 1 HETATM 25 C C4C HEM . . . E 3 -216.312 395.147 -105.555 1 34.17 ? C4C HEM 602 B 1 HETATM 26 C CMC HEM . . . E 3 -214.965 397.723 -103.163 1 34.09 ? CMC HEM 602 B 1 HETATM 27 C CAC HEM . . . E 3 -216.127 394.7 -102.939 1 33.93 ? CAC HEM 602 B 1 HETATM 28 C CBC HEM . . . E 3 -215.137 394.541 -102.057 1 33.84 ? CBC HEM 602 B 1 HETATM 29 C C1D HEM . . . E 3 -217.003 393.36 -107.1 1 34.27 ? C1D HEM 602 B 1 HETATM 30 C C2D HEM . . . E 3 -217.278 391.966 -107.364 1 34.25 ? C2D HEM 602 B 1 HETATM 31 C C3D HEM . . . E 3 -217.423 391.845 -108.873 1 34.35 ? C3D HEM 602 B 1 HETATM 32 C C4D HEM . . . E 3 -217.229 393.191 -109.333 1 34.41 ? C4D HEM 602 B 1 HETATM 33 C CMD HEM . . . E 3 -217.39 390.813 -106.351 1 34.19 ? CMD HEM 602 B 1 HETATM 34 C CAD HEM . . . E 3 -217.74 390.574 -109.7 1 34.41 ? CAD HEM 602 B 1 HETATM 35 C CBD HEM . . . E 3 -216.569 390.101 -110.557 1 34.48 ? CBD HEM 602 B 1 HETATM 36 C CGD HEM . . . E 3 -217.098 389.241 -111.682 1 34.63 ? CGD HEM 602 B 1 HETATM 37 O O1D HEM . . . E 3 -218.319 389.345 -111.987 1 34.59 ? O1D HEM 602 B 1 HETATM 38 O O2D HEM . . . E 3 -216.302 388.462 -112.28 1 34.66 ? O2D HEM 602 B 1 HETATM 39 N NA HEM . . . E 3 -216.313 395.805 -110.438 1 34.56 ? NA HEM 602 B 1 HETATM 40 N NB HEM . . . E 3 -215.439 397.872 -108.549 1 34.47 ? NB HEM 602 B 1 HETATM 41 N NC HEM . . . E 3 -216.062 396.165 -106.447 1 34.26 ? NC HEM 602 B 1 HETATM 42 N ND HEM . . . E 3 -216.954 394.049 -108.285 1 34.37 ? ND HEM 602 B 1 HETATM 43 FE FE HEM . . . E 3 -216.191 395.975 -108.406 1 34.39 ? FE HEM 602 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #