data_3GPH # _model_server_result.job_id 1aF9T5xmFrk2j3dIrwFqAg _model_server_result.datetime_utc '2024-10-17 18:25:42' _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 3gph # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 3GPH # _exptl.entry_id 3GPH _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 3GPH _cell.length_a 70.709 _cell.length_b 70.709 _cell.length_c 222.823 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GPH _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,G 1 1 B,E,F,H 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 ? 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 metalc ? metalc1 A SG CYS 416 A CYS 437 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 C FE HEM . A HEM 500 1_555 D N15 OID . A OID 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc3 B SG CYS 416 B CYS 437 1_555 E FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 E FE HEM . B HEM 500 1_555 F N15 OID . B OID 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _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 3GPH _atom_sites.fract_transf_matrix[1][1] 0.014142 _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] 0.014142 _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] 0.004488 _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 1 500 500 HEM HEM . D 3 OID A 1 501 501 OID OID . E 2 HEM B 1 500 500 HEM HEM . F 3 OID B 1 501 501 OID OID . G 4 HOH A 1 3 3 HOH HOH . G 4 HOH A 2 7 7 HOH HOH . G 4 HOH A 3 8 8 HOH HOH . G 4 HOH A 4 9 9 HOH HOH . G 4 HOH A 5 14 14 HOH HOH . G 4 HOH A 6 15 15 HOH HOH . G 4 HOH A 7 16 16 HOH HOH . G 4 HOH A 8 17 17 HOH HOH . G 4 HOH A 9 18 18 HOH HOH . G 4 HOH A 10 20 20 HOH HOH . G 4 HOH A 11 21 21 HOH HOH . G 4 HOH A 12 498 23 HOH HOH . G 4 HOH A 13 499 25 HOH HOH . G 4 HOH A 14 502 31 HOH HOH . G 4 HOH A 15 503 34 HOH HOH . H 4 HOH B 1 2 2 HOH HOH . H 4 HOH B 2 5 5 HOH HOH . H 4 HOH B 3 19 19 HOH HOH . H 4 HOH B 4 498 22 HOH HOH . H 4 HOH B 5 499 24 HOH HOH . H 4 HOH B 6 502 27 HOH HOH . H 4 HOH B 7 503 28 HOH HOH . H 4 HOH B 8 504 29 HOH HOH . H 4 HOH B 9 505 32 HOH HOH . H 4 HOH B 10 506 33 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 28.742 29.021 15.83 1 24.46 ? CHA HEM 500 B 1 HETATM 2 C CHB HEM . . . E 2 32.805 31.582 16.693 1 22.86 ? CHB HEM 500 B 1 HETATM 3 C CHC HEM . . . E 2 30.155 35.435 17.864 1 22.89 ? CHC HEM 500 B 1 HETATM 4 C CHD HEM . . . E 2 26.085 32.814 17.376 1 23.87 ? CHD HEM 500 B 1 HETATM 5 C C1A HEM . . . E 2 30.07 29.372 15.928 1 25.22 ? C1A HEM 500 B 1 HETATM 6 C C2A HEM . . . E 2 31.19 28.538 15.56 1 26.27 ? C2A HEM 500 B 1 HETATM 7 C C3A HEM . . . E 2 32.327 29.243 15.78 1 25.21 ? C3A HEM 500 B 1 HETATM 8 C C4A HEM . . . E 2 31.954 30.558 16.298 1 24.54 ? C4A HEM 500 B 1 HETATM 9 C CMA HEM . . . E 2 33.774 28.778 15.542 1 21.94 ? CMA HEM 500 B 1 HETATM 10 C CAA HEM . . . E 2 31.022 27.1 15.007 1 26.82 ? CAA HEM 500 B 1 HETATM 11 C CBA HEM . . . E 2 31.325 26.996 13.511 1 29.2 ? CBA HEM 500 B 1 HETATM 12 C CGA HEM . . . E 2 31.359 25.549 13.072 1 30.54 ? CGA HEM 500 B 1 HETATM 13 O O1A HEM . . . E 2 32.063 25.197 12.088 1 29.54 ? O1A HEM 500 B 1 HETATM 14 O O2A HEM . . . E 2 30.659 24.722 13.711 1 34.18 ? O2A HEM 500 B 1 HETATM 15 C C1B HEM . . . E 2 32.481 32.884 17.071 1 23.88 ? C1B HEM 500 B 1 HETATM 16 C C2B HEM . . . E 2 33.385 34.013 17.228 1 20.83 ? C2B HEM 500 B 1 HETATM 17 C C3B HEM . . . E 2 32.659 35.085 17.556 1 20.51 ? C3B HEM 500 B 1 HETATM 18 C C4B HEM . . . E 2 31.267 34.67 17.61 1 22.06 ? C4B HEM 500 B 1 HETATM 19 C CMB HEM . . . E 2 34.91 33.977 17.061 1 18.31 ? CMB HEM 500 B 1 HETATM 20 C CAB HEM . . . E 2 33.239 36.495 17.835 1 18.07 ? CAB HEM 500 B 1 HETATM 21 C CBB HEM . . . E 2 32.673 37.346 18.67 1 13.55 ? CBB HEM 500 B 1 HETATM 22 C C1C HEM . . . E 2 28.819 35.079 17.769 1 24.21 ? C1C HEM 500 B 1 HETATM 23 C C2C HEM . . . E 2 27.7 35.959 17.915 1 22.58 ? C2C HEM 500 B 1 HETATM 24 C C3C HEM . . . E 2 26.57 35.225 17.784 1 22.12 ? C3C HEM 500 B 1 HETATM 25 C C4C HEM . . . E 2 26.94 33.873 17.546 1 22.8 ? C4C HEM 500 B 1 HETATM 26 C CMC HEM . . . E 2 27.903 37.469 18.155 1 22.03 ? CMC HEM 500 B 1 HETATM 27 C CAC HEM . . . E 2 25.086 35.625 17.85 1 21.26 ? CAC HEM 500 B 1 HETATM 28 C CBC HEM . . . E 2 24.626 36.779 17.398 1 19.48 ? CBC HEM 500 B 1 HETATM 29 C C1D HEM . . . E 2 26.398 31.554 16.908 1 24.73 ? C1D HEM 500 B 1 HETATM 30 C C2D HEM . . . E 2 25.461 30.518 16.609 1 25.15 ? C2D HEM 500 B 1 HETATM 31 C C3D HEM . . . E 2 26.278 29.341 16.112 1 24.74 ? C3D HEM 500 B 1 HETATM 32 C C4D HEM . . . E 2 27.637 29.774 16.166 1 24.91 ? C4D HEM 500 B 1 HETATM 33 C CMD HEM . . . E 2 23.931 30.576 16.753 1 26.83 ? CMD HEM 500 B 1 HETATM 34 C CAD HEM . . . E 2 25.719 27.978 15.692 1 25.43 ? CAD HEM 500 B 1 HETATM 35 C CBD HEM . . . E 2 26.113 27.624 14.263 1 27 ? CBD HEM 500 B 1 HETATM 36 C CGD HEM . . . E 2 25.417 26.337 13.874 1 27.78 ? CGD HEM 500 B 1 HETATM 37 O O1D HEM . . . E 2 24.548 26.357 12.95 1 26.56 ? O1D HEM 500 B 1 HETATM 38 O O2D HEM . . . E 2 25.726 25.293 14.503 1 26.07 ? O2D HEM 500 B 1 HETATM 39 N NA HEM . . . E 2 30.574 30.576 16.369 1 24.73 ? NA HEM 500 B 1 HETATM 40 N NB HEM . . . E 2 31.212 33.349 17.333 1 23.37 ? NB HEM 500 B 1 HETATM 41 N NC HEM . . . E 2 28.298 33.833 17.553 1 24.46 ? NC HEM 500 B 1 HETATM 42 N ND HEM . . . E 2 27.647 31.064 16.644 1 24.32 ? ND HEM 500 B 1 HETATM 43 FE FE HEM . . . E 2 29.385 32.308 16.908 1 35.32 ? FE HEM 500 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 43 #