data_3GYS # _model_server_result.job_id 7KdYO0rZsvAqyJlSdJvWcw _model_server_result.datetime_utc '2024-12-11 03:05:50' _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 3gys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":143}' # _entry.id 3GYS # _exptl.entry_id 3GYS _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 8 _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 3GYS _cell.length_a 86.022 _cell.length_b 96.465 _cell.length_c 146.345 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GYS _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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L,Q,R,S 1 1 E,F,G,H,M,N,O,P,T,U,V,W 2 1 A,B,I,J,Q 3 1 C,D,K,L,R,S 4 1 E,F,M,N,T,U 5 1 G,H,O,P,V,W 6 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 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P 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 NE2 HIS 87 A HIS 87 1_555 I FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc2 Q O HOH . A HOH 142 1_555 I FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc3 B NE2 HIS 91 B HIS 92 1_555 J FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc4 C NE2 HIS 87 C HIS 87 1_555 K FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc5 R O HOH . C HOH 142 1_555 K FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc6 D NE2 HIS 91 D HIS 92 1_555 L FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc7 E NE2 HIS 87 E HIS 87 1_555 M FE HEM . E HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc8 T O HOH . E HOH 142 1_555 M FE HEM . E HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc9 F NE2 HIS 91 F HIS 92 1_555 N FE HEM . F HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc10 U O HOH . F HOH 147 1_555 N FE HEM . F HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc11 G NE2 HIS 87 G HIS 87 1_555 O FE HEM . G HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc12 O FE HEM . G HEM 143 1_555 V O HOH . G HOH 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc13 H NE2 HIS 91 H HIS 92 1_555 P FE HEM . H HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? # _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 3GYS _atom_sites.fract_transf_matrix[1][1] 0.011625 _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] 0.010366 _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] 0.006833 _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 I 3 HEM A 1 143 143 HEM HEM . J 3 HEM B 1 148 148 HEM HEM . K 3 HEM C 1 143 143 HEM HEM . L 3 HEM D 1 148 148 HEM HEM . M 3 HEM E 1 143 143 HEM HEM . N 3 HEM F 1 148 148 HEM HEM . O 3 HEM G 1 143 143 HEM HEM . P 3 HEM H 1 148 148 HEM HEM . Q 4 HOH A 1 142 10 HOH HOH . R 4 HOH C 1 142 1 HOH HOH . S 4 HOH D 1 147 5 HOH HOH . T 4 HOH E 1 142 6 HOH HOH . U 4 HOH F 1 147 4 HOH HOH . U 4 HOH F 2 149 8 HOH HOH . V 4 HOH G 1 142 2 HOH HOH . V 4 HOH G 2 144 3 HOH HOH . W 4 HOH H 1 147 9 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 . . . I 3 -23.96 -30.826 24.52 1 40.53 ? CHA HEM 143 A 1 HETATM 2 C CHB HEM . . . I 3 -21.323 -34.749 23.526 1 39.04 ? CHB HEM 143 A 1 HETATM 3 C CHC HEM . . . I 3 -17.417 -31.943 23.11 1 37.91 ? CHC HEM 143 A 1 HETATM 4 C CHD HEM . . . I 3 -20 -27.963 24.261 1 38.01 ? CHD HEM 143 A 1 HETATM 5 C C1A HEM . . . I 3 -23.555 -32.126 24.366 1 42.15 ? C1A HEM 143 A 1 HETATM 6 C C2A HEM . . . I 3 -24.355 -33.29 24.672 1 44.53 ? C2A HEM 143 A 1 HETATM 7 C C3A HEM . . . I 3 -23.633 -34.384 24.404 1 41.94 ? C3A HEM 143 A 1 HETATM 8 C C4A HEM . . . I 3 -22.352 -33.945 23.903 1 39.59 ? C4A HEM 143 A 1 HETATM 9 C CMA HEM . . . I 3 -24.099 -35.837 24.606 1 40.66 ? CMA HEM 143 A 1 HETATM 10 C CAA HEM . . . I 3 -25.774 -33.277 25.268 1 48.01 ? CAA HEM 143 A 1 HETATM 11 C CBA HEM . . . I 3 -26.846 -32.626 24.416 1 52.75 ? CBA HEM 143 A 1 HETATM 12 C CGA HEM . . . I 3 -28.12 -33.068 25.09 1 55.8 ? CGA HEM 143 A 1 HETATM 13 O O1A HEM . . . I 3 -29.125 -33.326 24.375 1 55.88 ? O1A HEM 143 A 1 HETATM 14 O O2A HEM . . . I 3 -28.105 -33.181 26.357 1 58.86 ? O2A HEM 143 A 1 HETATM 15 C C1B HEM . . . I 3 -20.016 -34.345 23.364 1 38.41 ? C1B HEM 143 A 1 HETATM 16 C C2B HEM . . . I 3 -18.899 -35.217 23.082 1 36.84 ? C2B HEM 143 A 1 HETATM 17 C C3B HEM . . . I 3 -17.809 -34.45 22.949 1 35.09 ? C3B HEM 143 A 1 HETATM 18 C C4B HEM . . . I 3 -18.209 -33.073 23.146 1 35.75 ? C4B HEM 143 A 1 HETATM 19 C CMB HEM . . . I 3 -19.011 -36.76 22.96 1 34.39 ? CMB HEM 143 A 1 HETATM 20 C CAB HEM . . . I 3 -16.374 -34.961 22.656 1 34.54 ? CAB HEM 143 A 1 HETATM 21 C CBB HEM . . . I 3 -16.074 -36.269 22.565 1 32.53 ? CBB HEM 143 A 1 HETATM 22 C C1C HEM . . . I 3 -17.765 -30.634 23.439 1 38.54 ? C1C HEM 143 A 1 HETATM 23 C C2C HEM . . . I 3 -16.842 -29.524 23.616 1 38.17 ? C2C HEM 143 A 1 HETATM 24 C C3C HEM . . . I 3 -17.551 -28.416 23.939 1 38.77 ? C3C HEM 143 A 1 HETATM 25 C C4C HEM . . . I 3 -18.953 -28.791 23.973 1 38.39 ? C4C HEM 143 A 1 HETATM 26 C CMC HEM . . . I 3 -15.318 -29.614 23.45 1 37.66 ? CMC HEM 143 A 1 HETATM 27 C CAC HEM . . . I 3 -16.999 -26.987 24.231 1 38.34 ? CAC HEM 143 A 1 HETATM 28 C CBC HEM . . . I 3 -16.257 -26.713 25.316 1 35.81 ? CBC HEM 143 A 1 HETATM 29 C C1D HEM . . . I 3 -21.304 -28.351 24.443 1 39.7 ? C1D HEM 143 A 1 HETATM 30 C C2D HEM . . . I 3 -22.401 -27.481 24.815 1 41.55 ? C2D HEM 143 A 1 HETATM 31 C C3D HEM . . . I 3 -23.637 -28.376 24.903 1 43.14 ? C3D HEM 143 A 1 HETATM 32 C C4D HEM . . . I 3 -23.159 -29.704 24.569 1 41.76 ? C4D HEM 143 A 1 HETATM 33 C CMD HEM . . . I 3 -22.363 -25.962 25.087 1 43.43 ? CMD HEM 143 A 1 HETATM 34 C CAD HEM . . . I 3 -25.081 -27.953 25.268 1 44.79 ? CAD HEM 143 A 1 HETATM 35 C CBD HEM . . . I 3 -25.176 -27.766 26.782 1 48.15 ? CBD HEM 143 A 1 HETATM 36 C CGD HEM . . . I 3 -26.569 -27.327 27.18 1 51.22 ? CGD HEM 143 A 1 HETATM 37 O O1D HEM . . . I 3 -27.225 -28.137 27.891 1 51.49 ? O1D HEM 143 A 1 HETATM 38 O O2D HEM . . . I 3 -27.024 -26.194 26.803 1 52.49 ? O2D HEM 143 A 1 HETATM 39 N NA HEM . . . I 3 -22.33 -32.571 23.897 1 39.96 ? NA HEM 143 A 1 HETATM 40 N NB HEM . . . I 3 -19.557 -33.045 23.394 1 38.1 ? NB HEM 143 A 1 HETATM 41 N NC HEM . . . I 3 -19.054 -30.139 23.659 1 39.29 ? NC HEM 143 A 1 HETATM 42 N ND HEM . . . I 3 -21.79 -29.64 24.304 1 39.83 ? ND HEM 143 A 1 HETATM 43 FE FE HEM . . . I 3 -20.743 -31.315 23.976 1 39.93 ? FE HEM 143 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #