data_5VEU # _model_server_result.job_id GdbkzT75GktcS1mpmO9YGw _model_server_result.datetime_utc '2024-11-23 19:38:02' _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 5veu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":601}' # _entry.id 5VEU # _exptl.entry_id 5VEU _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 12 _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 5VEU _cell.length_a 148.988 _cell.length_b 198.384 _cell.length_c 234.881 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VEU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 ? monomeric 1 author_defined_assembly 7 ? monomeric 1 author_defined_assembly 8 ? monomeric 1 author_defined_assembly 9 ? monomeric 1 author_defined_assembly 10 ? monomeric 1 author_defined_assembly 11 ? monomeric 1 author_defined_assembly 12 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,M,N 1 1 B,O,P 2 1 C,Q 3 1 D,R 4 1 E,S 5 1 F,T 6 1 G,U 7 1 H,V,W 8 1 I,X 9 1 J,Y 10 1 K,Z 11 1 L,AA 12 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 M N N ? 2 O N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 X N N ? 2 Y N N ? 2 Z N N ? 2 AA 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 SG CYS 420 A CYS 441 1_555 M FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 M FE HEM . A HEM 601 1_555 N N5 RIT . A RIT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 B SG CYS 420 B CYS 441 1_555 O FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc4 O FE HEM . B HEM 601 1_555 P N5 RIT . B RIT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc5 C SG CYS 420 C CYS 441 1_555 Q FE HEM . C HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 D SG CYS 420 D CYS 441 1_555 R FE HEM . D HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc7 E SG CYS 420 E CYS 441 1_555 S FE HEM . E HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc8 F SG CYS 420 F CYS 441 1_555 T FE HEM . F HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc9 G SG CYS 420 G CYS 441 1_555 U FE HEM . G HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc10 H SG CYS 420 H CYS 441 1_555 V FE HEM . H HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc11 V FE HEM . H HEM 601 1_555 W N5 RIT . H RIT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc12 I SG CYS 420 I CYS 441 1_555 X FE HEM . I HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc13 J SG CYS 420 J CYS 441 1_555 Y FE HEM . J HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc14 K SG CYS 420 K CYS 441 1_555 Z FE HEM . K HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc15 L SG CYS 420 L CYS 441 1_555 AA FE HEM . L HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? # _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 5VEU _atom_sites.fract_transf_matrix[1][1] 0.006712 _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] 0.005041 _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] 0.004257 _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 M 2 HEM A 1 601 500 HEM HEM . N 3 RIT A 1 602 501 RIT RIT . O 2 HEM B 1 601 500 HEM HEM . P 3 RIT B 1 602 501 RIT RIT . Q 2 HEM C 1 601 500 HEM HEM . R 2 HEM D 1 601 500 HEM HEM . S 2 HEM E 1 601 500 HEM HEM . T 2 HEM F 1 601 500 HEM HEM . U 2 HEM G 1 601 500 HEM HEM . V 2 HEM H 1 601 500 HEM HEM . W 3 RIT H 1 602 501 RIT RIT . X 2 HEM I 1 601 500 HEM HEM . Y 2 HEM J 1 601 500 HEM HEM . Z 2 HEM K 1 601 500 HEM HEM . AA 2 HEM L 1 601 500 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 . . . O 2 10.466 -60.971 92.953 1 49.87 ? CHA HEM 601 B 1 HETATM 2 C CHB HEM . . . O 2 14.389 -59.343 90.59 1 50.44 ? CHB HEM 601 B 1 HETATM 3 C CHC HEM . . . O 2 11.547 -57.597 87.069 1 43.35 ? CHC HEM 601 B 1 HETATM 4 C CHD HEM . . . O 2 7.645 -59.424 89.305 1 44.45 ? CHD HEM 601 B 1 HETATM 5 C C1A HEM . . . O 2 11.769 -60.636 92.653 1 48.67 ? C1A HEM 601 B 1 HETATM 6 C C2A HEM . . . O 2 12.923 -60.82 93.509 1 46.69 ? C2A HEM 601 B 1 HETATM 7 C C3A HEM . . . O 2 14 -60.37 92.862 1 46.23 ? C3A HEM 601 B 1 HETATM 8 C C4A HEM . . . O 2 13.577 -59.886 91.563 1 48.15 ? C4A HEM 601 B 1 HETATM 9 C CMA HEM . . . O 2 15.413 -60.368 93.387 1 45.28 ? CMA HEM 601 B 1 HETATM 10 C CAA HEM . . . O 2 12.902 -61.421 94.929 1 38.11 ? CAA HEM 601 B 1 HETATM 11 C CBA HEM . . . O 2 13.153 -62.921 94.892 1 54.99 ? CBA HEM 601 B 1 HETATM 12 C CGA HEM . . . O 2 13.151 -63.438 96.306 1 60.34 ? CGA HEM 601 B 1 HETATM 13 O O1A HEM . . . O 2 13.306 -64.672 96.491 1 47.93 ? O1A HEM 601 B 1 HETATM 14 O O2A HEM . . . O 2 12.993 -62.618 97.249 1 56.73 ? O2A HEM 601 B 1 HETATM 15 C C1B HEM . . . O 2 13.97 -58.754 89.416 1 49.85 ? C1B HEM 601 B 1 HETATM 16 C C2B HEM . . . O 2 14.829 -58.216 88.378 1 43.02 ? C2B HEM 601 B 1 HETATM 17 C C3B HEM . . . O 2 14.044 -57.731 87.397 1 44.84 ? C3B HEM 601 B 1 HETATM 18 C C4B HEM . . . O 2 12.665 -57.95 87.795 1 47.22 ? C4B HEM 601 B 1 HETATM 19 C CMB HEM . . . O 2 16.338 -58.239 88.454 1 48.7 ? CMB HEM 601 B 1 HETATM 20 C CAB HEM . . . O 2 14.426 -57.047 86.055 1 42.82 ? CAB HEM 601 B 1 HETATM 21 C CBB HEM . . . O 2 15.673 -56.816 85.624 1 41.67 ? CBB HEM 601 B 1 HETATM 22 C C1C HEM . . . O 2 10.244 -57.956 87.352 1 40.88 ? C1C HEM 601 B 1 HETATM 23 C C2C HEM . . . O 2 9.086 -57.682 86.52 1 42.78 ? C2C HEM 601 B 1 HETATM 24 C C3C HEM . . . O 2 8.001 -58.188 87.138 1 45.02 ? C3C HEM 601 B 1 HETATM 25 C C4C HEM . . . O 2 8.45 -58.794 88.378 1 44.6 ? C4C HEM 601 B 1 HETATM 26 C CMC HEM . . . O 2 9.171 -56.949 85.202 1 42.24 ? CMC HEM 601 B 1 HETATM 27 C CAC HEM . . . O 2 6.508 -58.186 86.708 1 43.94 ? CAC HEM 601 B 1 HETATM 28 C CBC HEM . . . O 2 6.033 -57.651 85.577 1 42.87 ? CBC HEM 601 B 1 HETATM 29 C C1D HEM . . . O 2 8.058 -59.958 90.508 1 43.94 ? C1D HEM 601 B 1 HETATM 30 C C2D HEM . . . O 2 7.2 -60.476 91.554 1 46.41 ? C2D HEM 601 B 1 HETATM 31 C C3D HEM . . . O 2 7.973 -60.9 92.558 1 47.66 ? C3D HEM 601 B 1 HETATM 32 C C4D HEM . . . O 2 9.356 -60.671 92.189 1 47.73 ? C4D HEM 601 B 1 HETATM 33 C CMD HEM . . . O 2 5.696 -60.518 91.503 1 39.57 ? CMD HEM 601 B 1 HETATM 34 C CAD HEM . . . O 2 7.49 -61.533 93.883 1 51.32 ? CAD HEM 601 B 1 HETATM 35 C CBD HEM . . . O 2 7.094 -62.986 93.638 1 55.33 ? CBD HEM 601 B 1 HETATM 36 C CGD HEM . . . O 2 6.554 -63.597 94.905 1 54.9 ? CGD HEM 601 B 1 HETATM 37 O O1D HEM . . . O 2 5.87 -64.649 94.817 1 52.95 ? O1D HEM 601 B 1 HETATM 38 O O2D HEM . . . O 2 6.8 -63.029 96.001 1 52.67 ? O2D HEM 601 B 1 HETATM 39 N NA HEM . . . O 2 12.208 -60.066 91.473 1 47.44 ? NA HEM 601 B 1 HETATM 40 N NB HEM . . . O 2 12.657 -58.574 89.028 1 49.44 ? NB HEM 601 B 1 HETATM 41 N NC HEM . . . O 2 9.819 -58.636 88.477 1 37.95 ? NC HEM 601 B 1 HETATM 42 N ND HEM . . . O 2 9.367 -60.094 90.932 1 46.78 ? ND HEM 601 B 1 HETATM 43 FE FE HEM . . . O 2 11.008 -59.38 89.977 1 60.67 3 FE HEM 601 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 64 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #