data_4Q5P # _model_server_result.job_id YXYNF1AHt3y9kJVHGSK1BQ _model_server_result.datetime_utc '2024-10-14 08:24:53' _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 4q5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4Q5P # _exptl.entry_id 4Q5P _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 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 4Q5P _cell.length_a 106.02 _cell.length_b 106.02 _cell.length_c 149.84 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q5P _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1,2 B,E,H 2 1,3 C,F,I 3 1,4 # 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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 149.84 3 'crystal symmetry operation' 16_555 -y+1/2,-x+1/2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 53.01 53.01 74.92 4 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 106.02 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F 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 81 A CYS 78 1_555 A SG CYS 81 A CYS 78 7_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf2 B SG CYS 81 B CYS 78 1_555 B SG CYS 81 B CYS 78 16_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? disulf ? disulf3 C SG CYS 81 C CYS 78 1_555 C SG CYS 81 C CYS 78 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc1 A NE2 HIS 21 A HIS 18 1_555 D FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc2 A NZ LYS 76 A LYS 73 1_555 D FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc3 B NE2 HIS 21 B HIS 18 1_555 E FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc4 B NZ LYS 76 B LYS 73 1_555 E FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc5 C NE2 HIS 21 C HIS 18 1_555 F FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc6 C NZ LYS 76 C LYS 73 1_555 F FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? # _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 4Q5P _atom_sites.fract_transf_matrix[1][1] 0.009432 _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] 0.009432 _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] 0.006674 _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 HEM A 1 201 105 HEM HEM . E 2 HEM B 1 201 105 HEM HEM . F 2 HEM C 1 201 105 HEM HEM . G 3 HOH A 1 301 1 HOH HOH . G 3 HOH A 2 302 2 HOH HOH . G 3 HOH A 3 303 3 HOH HOH . G 3 HOH A 4 304 4 HOH HOH . G 3 HOH A 5 305 7 HOH HOH . G 3 HOH A 6 306 8 HOH HOH . G 3 HOH A 7 307 12 HOH HOH . G 3 HOH A 8 308 13 HOH HOH . G 3 HOH A 9 309 17 HOH HOH . G 3 HOH A 10 310 19 HOH HOH . G 3 HOH A 11 311 20 HOH HOH . G 3 HOH A 12 312 23 HOH HOH . G 3 HOH A 13 313 25 HOH HOH . G 3 HOH A 14 314 26 HOH HOH . G 3 HOH A 15 315 33 HOH HOH . G 3 HOH A 16 316 36 HOH HOH . G 3 HOH A 17 317 38 HOH HOH . G 3 HOH A 18 318 40 HOH HOH . G 3 HOH A 19 319 41 HOH HOH . G 3 HOH A 20 320 43 HOH HOH . G 3 HOH A 21 321 44 HOH HOH . G 3 HOH A 22 322 45 HOH HOH . G 3 HOH A 23 323 47 HOH HOH . G 3 HOH A 24 324 48 HOH HOH . G 3 HOH A 25 325 50 HOH HOH . G 3 HOH A 26 326 52 HOH HOH . G 3 HOH A 27 327 53 HOH HOH . G 3 HOH A 28 328 54 HOH HOH . G 3 HOH A 29 329 58 HOH HOH . G 3 HOH A 30 330 59 HOH HOH . G 3 HOH A 31 331 60 HOH HOH . G 3 HOH A 32 332 61 HOH HOH . G 3 HOH A 33 333 65 HOH HOH . G 3 HOH A 34 334 68 HOH HOH . G 3 HOH A 35 335 77 HOH HOH . H 3 HOH B 1 301 10 HOH HOH . H 3 HOH B 2 302 11 HOH HOH . H 3 HOH B 3 303 14 HOH HOH . H 3 HOH B 4 304 21 HOH HOH . H 3 HOH B 5 305 24 HOH HOH . H 3 HOH B 6 306 27 HOH HOH . H 3 HOH B 7 307 30 HOH HOH . H 3 HOH B 8 308 37 HOH HOH . H 3 HOH B 9 309 62 HOH HOH . H 3 HOH B 10 310 64 HOH HOH . H 3 HOH B 11 311 70 HOH HOH . H 3 HOH B 12 312 71 HOH HOH . H 3 HOH B 13 313 73 HOH HOH . H 3 HOH B 14 314 74 HOH HOH . H 3 HOH B 15 315 75 HOH HOH . H 3 HOH B 16 316 78 HOH HOH . H 3 HOH B 17 317 79 HOH HOH . H 3 HOH B 18 318 82 HOH HOH . H 3 HOH B 19 319 83 HOH HOH . H 3 HOH B 20 320 84 HOH HOH . H 3 HOH B 21 321 86 HOH HOH . H 3 HOH B 22 322 87 HOH HOH . I 3 HOH C 1 301 5 HOH HOH . I 3 HOH C 2 302 6 HOH HOH . I 3 HOH C 3 303 9 HOH HOH . I 3 HOH C 4 304 15 HOH HOH . I 3 HOH C 5 305 16 HOH HOH . I 3 HOH C 6 306 18 HOH HOH . I 3 HOH C 7 307 22 HOH HOH . I 3 HOH C 8 308 28 HOH HOH . I 3 HOH C 9 309 29 HOH HOH . I 3 HOH C 10 310 31 HOH HOH . I 3 HOH C 11 311 32 HOH HOH . I 3 HOH C 12 312 34 HOH HOH . I 3 HOH C 13 313 35 HOH HOH . I 3 HOH C 14 314 39 HOH HOH . I 3 HOH C 15 315 42 HOH HOH . I 3 HOH C 16 316 46 HOH HOH . I 3 HOH C 17 317 49 HOH HOH . I 3 HOH C 18 318 51 HOH HOH . I 3 HOH C 19 319 55 HOH HOH . I 3 HOH C 20 320 56 HOH HOH . I 3 HOH C 21 321 57 HOH HOH . I 3 HOH C 22 322 63 HOH HOH . I 3 HOH C 23 323 66 HOH HOH . I 3 HOH C 24 324 67 HOH HOH . I 3 HOH C 25 325 69 HOH HOH . I 3 HOH C 26 326 72 HOH HOH . I 3 HOH C 27 327 80 HOH HOH . I 3 HOH C 28 328 81 HOH HOH . I 3 HOH C 29 329 85 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 18.372 45.323 31.892 1 20.88 ? CHA HEM 201 B 1 HETATM 2 C CHB HEM . . . E 2 21.521 48.408 33.95 1 30.49 ? CHB HEM 201 B 1 HETATM 3 C CHC HEM . . . E 2 17.889 49.929 36.874 1 29.3 ? CHC HEM 201 B 1 HETATM 4 C CHD HEM . . . E 2 15.381 45.926 35.694 1 27.02 ? CHD HEM 201 B 1 HETATM 5 C C1A HEM . . . E 2 19.524 46.025 32.199 1 19 ? C1A HEM 201 B 1 HETATM 6 C C2A HEM . . . E 2 20.777 45.881 31.523 1 26.87 ? C2A HEM 201 B 1 HETATM 7 C C3A HEM . . . E 2 21.671 46.735 32.104 1 24.9 ? C3A HEM 201 B 1 HETATM 8 C C4A HEM . . . E 2 20.967 47.432 33.13 1 29.9 ? C4A HEM 201 B 1 HETATM 9 C CMA HEM . . . E 2 23.134 46.87 31.732 1 31.77 ? CMA HEM 201 B 1 HETATM 10 C CAA HEM . . . E 2 21.09 44.932 30.378 1 25.84 ? CAA HEM 201 B 1 HETATM 11 C CBA HEM . . . E 2 21.671 43.625 30.92 1 21.08 ? CBA HEM 201 B 1 HETATM 12 C CGA HEM . . . E 2 22.178 42.766 29.792 1 22.98 ? CGA HEM 201 B 1 HETATM 13 O O1A HEM . . . E 2 22.611 41.631 30.063 1 26.44 ? O1A HEM 201 B 1 HETATM 14 O O2A HEM . . . E 2 22.171 43.188 28.611 1 24.18 ? O2A HEM 201 B 1 HETATM 15 C C1B HEM . . . E 2 20.75 49.173 34.858 1 34.2 ? C1B HEM 201 B 1 HETATM 16 C C2B HEM . . . E 2 21.155 50.463 35.354 1 40.52 ? C2B HEM 201 B 1 HETATM 17 C C3B HEM . . . E 2 20.151 50.931 36.17 1 36.88 ? C3B HEM 201 B 1 HETATM 18 C C4B HEM . . . E 2 19.093 49.863 36.144 1 31.96 ? C4B HEM 201 B 1 HETATM 19 C CMB HEM . . . E 2 22.409 51.21 34.959 1 48.97 ? CMB HEM 201 B 1 HETATM 20 C CAB HEM . . . E 2 20.03 52.264 36.828 1 32.9 ? CAB HEM 201 B 1 HETATM 21 C CBB HEM . . . E 2 20.742 53.338 36.469 1 22.94 ? CBB HEM 201 B 1 HETATM 22 C C1C HEM . . . E 2 16.886 48.945 36.872 1 23.43 ? C1C HEM 201 B 1 HETATM 23 C C2C HEM . . . E 2 15.651 48.984 37.572 1 27.65 ? C2C HEM 201 B 1 HETATM 24 C C3C HEM . . . E 2 14.926 47.835 37.238 1 30.59 ? C3C HEM 201 B 1 HETATM 25 C C4C HEM . . . E 2 15.742 47.103 36.315 1 28.47 ? C4C HEM 201 B 1 HETATM 26 C CMC HEM . . . E 2 15.203 50.087 38.503 1 29.79 ? CMC HEM 201 B 1 HETATM 27 C CAC HEM . . . E 2 13.547 47.433 37.655 1 32.32 ? CAC HEM 201 B 1 HETATM 28 C CBC HEM . . . E 2 12.749 48.181 38.423 1 33.35 ? CBC HEM 201 B 1 HETATM 29 C C1D HEM . . . E 2 15.946 45.479 34.487 1 24.57 ? C1D HEM 201 B 1 HETATM 30 C C2D HEM . . . E 2 15.361 44.348 33.696 1 18.78 ? C2D HEM 201 B 1 HETATM 31 C C3D HEM . . . E 2 16.191 44.204 32.607 1 18.86 ? C3D HEM 201 B 1 HETATM 32 C C4D HEM . . . E 2 17.284 45.208 32.785 1 23.61 ? C4D HEM 201 B 1 HETATM 33 C CMD HEM . . . E 2 14.077 43.587 33.99 1 22.37 ? CMD HEM 201 B 1 HETATM 34 C CAD HEM . . . E 2 16.023 43.207 31.463 1 18.8 ? CAD HEM 201 B 1 HETATM 35 C CBD HEM . . . E 2 15.282 43.873 30.308 1 21.94 ? CBD HEM 201 B 1 HETATM 36 C CGD HEM . . . E 2 14.532 42.86 29.501 1 24.57 ? CGD HEM 201 B 1 HETATM 37 O O1D HEM . . . E 2 14.753 41.638 29.668 1 27.03 ? O1D HEM 201 B 1 HETATM 38 O O2D HEM . . . E 2 13.666 43.253 28.685 1 25.33 ? O2D HEM 201 B 1 HETATM 39 N NA HEM . . . E 2 19.641 47.016 33.154 1 24.04 ? NA HEM 201 B 1 HETATM 40 N NB HEM . . . E 2 19.518 48.877 35.336 1 36.18 ? NB HEM 201 B 1 HETATM 41 N NC HEM . . . E 2 16.866 47.845 36.072 1 24.88 ? NC HEM 201 B 1 HETATM 42 N ND HEM . . . E 2 17.093 45.949 33.919 1 24.04 ? ND HEM 201 B 1 HETATM 43 FE FE HEM . . . E 2 18.263 47.346 34.596 1 23.34 ? FE HEM 201 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #