data_2GKN # _model_server_result.job_id Rbea_mZuvyInXGFYpKZEjQ _model_server_result.datetime_utc '2024-11-23 21:33:07' _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 2gkn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":144}' # _entry.id 2GKN # _exptl.entry_id 2GKN _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 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 2GKN _cell.length_a 45.034 _cell.length_b 62.388 _cell.length_c 90.974 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GKN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 D N N ? 3 G 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 81 A HIS 81 1_555 D FE HEM . A HEM 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc2 D FE HEM . A HEM 144 1_555 C C CYN . A CYN 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 B NE2 HIS 81 B HIS 81 1_555 G FE HEM . B HEM 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc4 B O GLY 83 B GLY 83 1_555 E NA NA . B NA 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc5 G FE HEM . B HEM 144 1_555 F C CYN . B CYN 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc6 G FE HEM . B HEM 144 1_555 F N CYN . B CYN 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? # _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 117 n n CHA C4D HEM doub 118 n n CHA HHA HEM sing 119 n n CHB C4A HEM sing 120 n n CHB C1B HEM doub 121 n n CHB HHB HEM sing 122 n n CHC C4B HEM sing 123 n n CHC C1C HEM doub 124 n n CHC HHC HEM sing 125 n n CHD C4C HEM doub 126 n n CHD C1D HEM sing 127 n n CHD HHD HEM sing 128 n n C1A C2A HEM doub 129 n y C1A NA HEM sing 130 n y C2A C3A HEM sing 131 n y C2A CAA HEM sing 132 n n C3A C4A HEM doub 133 n y C3A CMA HEM sing 134 n n C4A NA HEM sing 135 n y CMA HMA HEM sing 136 n n CMA HMAA HEM sing 137 n n CMA HMAB HEM sing 138 n n CAA CBA HEM sing 139 n n CAA HAA HEM sing 140 n n CAA HAAA HEM sing 141 n n CBA CGA HEM sing 142 n n CBA HBA HEM sing 143 n n CBA HBAA HEM sing 144 n n CGA O1A HEM doub 145 n n CGA O2A HEM sing 146 n n C1B C2B HEM sing 147 n n C1B NB HEM sing 148 n n C2B C3B HEM doub 149 n n C2B CMB HEM sing 150 n n C3B C4B HEM sing 151 n n C3B CAB HEM sing 152 n n C4B NB HEM doub 153 n n CMB HMB HEM sing 154 n n CMB HMBA HEM sing 155 n n CMB HMBB HEM sing 156 n n CAB CBB HEM doub 157 n n CAB HAB HEM sing 158 n n CBB HBB HEM sing 159 n n CBB HBBA HEM sing 160 n n C1C C2C HEM sing 161 n y C1C NC HEM sing 162 n y C2C C3C HEM doub 163 n y C2C CMC HEM sing 164 n n C3C C4C HEM sing 165 n y C3C CAC HEM sing 166 n n C4C NC HEM sing 167 n y CMC HMC HEM sing 168 n n CMC HMCA HEM sing 169 n n CMC HMCB HEM sing 170 n n CAC CBC HEM doub 171 n n CAC HAC HEM sing 172 n n CBC HBC HEM sing 173 n n CBC HBCA HEM sing 174 n n C1D C2D HEM sing 175 n n C1D ND HEM doub 176 n n C2D C3D HEM doub 177 n n C2D CMD HEM sing 178 n n C3D C4D HEM sing 179 n n C3D CAD HEM sing 180 n n C4D ND HEM sing 181 n n CMD HMD HEM sing 182 n n CMD HMDA HEM sing 183 n n CMD HMDB HEM sing 184 n n CAD CBD HEM sing 185 n n CAD HAD HEM sing 186 n n CAD HADA HEM sing 187 n n CBD CGD HEM sing 188 n n CBD HBD HEM sing 189 n n CBD HBDA HEM sing 190 n n CGD O1D HEM doub 191 n n CGD O2D HEM sing 192 n n O2A H2A HEM sing 193 n n O2D H2D HEM sing 194 n n FE NA HEM sing 195 n n FE NB HEM sing 196 n n FE NC HEM sing 197 n n FE ND HEM sing 198 n n # _atom_sites.entry_id 2GKN _atom_sites.fract_transf_matrix[1][1] 0.022205 _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] 0.016029 _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] 0.010992 _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 CYN A 1 145 145 CYN CN . D 3 HEM A 1 144 144 HEM HEM . E 4 NA B 1 137 1 NA NA . F 2 CYN B 1 145 145 CYN CN . G 3 HEM B 1 144 144 HEM HEM . H 5 HOH A 1 146 2 HOH HOH . H 5 HOH A 2 147 3 HOH HOH . H 5 HOH A 3 148 4 HOH HOH . H 5 HOH A 4 149 5 HOH HOH . H 5 HOH A 5 150 9 HOH HOH . H 5 HOH A 6 151 11 HOH HOH . H 5 HOH A 7 152 12 HOH HOH . H 5 HOH A 8 153 13 HOH HOH . H 5 HOH A 9 154 14 HOH HOH . H 5 HOH A 10 155 15 HOH HOH . H 5 HOH A 11 156 16 HOH HOH . H 5 HOH A 12 157 17 HOH HOH . H 5 HOH A 13 158 18 HOH HOH . H 5 HOH A 14 159 19 HOH HOH . H 5 HOH A 15 160 20 HOH HOH . H 5 HOH A 16 161 23 HOH HOH . H 5 HOH A 17 162 24 HOH HOH . H 5 HOH A 18 163 26 HOH HOH . H 5 HOH A 19 164 31 HOH HOH . H 5 HOH A 20 165 32 HOH HOH . H 5 HOH A 21 166 35 HOH HOH . H 5 HOH A 22 167 36 HOH HOH . H 5 HOH A 23 168 40 HOH HOH . H 5 HOH A 24 169 43 HOH HOH . H 5 HOH A 25 170 46 HOH HOH . H 5 HOH A 26 171 47 HOH HOH . H 5 HOH A 27 172 48 HOH HOH . H 5 HOH A 28 173 49 HOH HOH . I 5 HOH B 1 146 6 HOH HOH . I 5 HOH B 2 147 7 HOH HOH . I 5 HOH B 3 148 8 HOH HOH . I 5 HOH B 4 149 10 HOH HOH . I 5 HOH B 5 150 21 HOH HOH . I 5 HOH B 6 151 22 HOH HOH . I 5 HOH B 7 152 25 HOH HOH . I 5 HOH B 8 153 27 HOH HOH . I 5 HOH B 9 154 28 HOH HOH . I 5 HOH B 10 155 29 HOH HOH . I 5 HOH B 11 156 30 HOH HOH . I 5 HOH B 12 157 33 HOH HOH . I 5 HOH B 13 158 34 HOH HOH . I 5 HOH B 14 159 37 HOH HOH . I 5 HOH B 15 160 38 HOH HOH . I 5 HOH B 16 161 39 HOH HOH . I 5 HOH B 17 162 41 HOH HOH . I 5 HOH B 18 163 42 HOH HOH . I 5 HOH B 19 164 44 HOH HOH . I 5 HOH B 20 165 45 HOH HOH . I 5 HOH B 21 166 50 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 . . . D 3 -16.172 21.539 -18.862 1 18.33 ? CHA HEM 144 A 1 HETATM 2 C CHB HEM . . . D 3 -14.825 20.781 -14.274 1 16.18 ? CHB HEM 144 A 1 HETATM 3 C CHC HEM . . . D 3 -18.144 17.244 -13.962 1 17.95 ? CHC HEM 144 A 1 HETATM 4 C CHD HEM . . . D 3 -18.773 17.375 -18.799 1 16.8 ? CHD HEM 144 A 1 HETATM 5 C C1A HEM . . . D 3 -15.54 21.682 -17.647 1 15.76 ? C1A HEM 144 A 1 HETATM 6 C C2A HEM . . . D 3 -14.563 22.697 -17.303 1 17.8 ? C2A HEM 144 A 1 HETATM 7 C C3A HEM . . . D 3 -14.184 22.486 -16.031 1 18.17 ? C3A HEM 144 A 1 HETATM 8 C C4A HEM . . . D 3 -14.919 21.336 -15.531 1 18.84 ? C4A HEM 144 A 1 HETATM 9 C CMA HEM . . . D 3 -13.158 23.314 -15.219 1 19.29 ? CMA HEM 144 A 1 HETATM 10 C CAA HEM . . . D 3 -14.046 23.807 -18.264 1 20.33 ? CAA HEM 144 A 1 HETATM 11 C CBA HEM . . . D 3 -14.949 25.032 -18.25 1 20.73 ? CBA HEM 144 A 1 HETATM 12 C CGA HEM . . . D 3 -14.532 25.985 -19.337 1 25.66 ? CGA HEM 144 A 1 HETATM 13 O O1A HEM . . . D 3 -14.399 27.203 -19.048 1 27.56 ? O1A HEM 144 A 1 HETATM 14 O O2A HEM . . . D 3 -14.334 25.535 -20.497 1 28.18 ? O2A HEM 144 A 1 HETATM 15 C C1B HEM . . . D 3 -15.631 19.782 -13.762 1 17.57 ? C1B HEM 144 A 1 HETATM 16 C C2B HEM . . . D 3 -15.668 19.316 -12.39 1 11.01 ? C2B HEM 144 A 1 HETATM 17 C C3B HEM . . . D 3 -16.584 18.342 -12.299 1 18.68 ? C3B HEM 144 A 1 HETATM 18 C C4B HEM . . . D 3 -17.161 18.149 -13.616 1 17.91 ? C4B HEM 144 A 1 HETATM 19 C CMB HEM . . . D 3 -14.797 19.85 -11.24 1 15.46 ? CMB HEM 144 A 1 HETATM 20 C CAB HEM . . . D 3 -16.971 17.555 -11.022 1 16.5 ? CAB HEM 144 A 1 HETATM 21 C CBB HEM . . . D 3 -16.828 16.227 -10.993 1 19.64 ? CBB HEM 144 A 1 HETATM 22 C C1C HEM . . . D 3 -18.553 16.919 -15.24 1 18.89 ? C1C HEM 144 A 1 HETATM 23 C C2C HEM . . . D 3 -19.366 15.782 -15.61 1 19.66 ? C2C HEM 144 A 1 HETATM 24 C C3C HEM . . . D 3 -19.548 15.81 -16.945 1 18.02 ? C3C HEM 144 A 1 HETATM 25 C C4C HEM . . . D 3 -18.842 16.969 -17.469 1 22.68 ? C4C HEM 144 A 1 HETATM 26 C CMC HEM . . . D 3 -19.918 14.75 -14.589 1 19.52 ? CMC HEM 144 A 1 HETATM 27 C CAC HEM . . . D 3 -20.357 14.801 -17.804 1 17.46 ? CAC HEM 144 A 1 HETATM 28 C CBC HEM . . . D 3 -20.13 13.481 -17.734 1 16.95 ? CBC HEM 144 A 1 HETATM 29 C C1D HEM . . . D 3 -18.086 18.471 -19.304 1 20.44 ? C1D HEM 144 A 1 HETATM 30 C C2D HEM . . . D 3 -17.876 18.802 -20.705 1 21.67 ? C2D HEM 144 A 1 HETATM 31 C C3D HEM . . . D 3 -17.069 20.108 -20.708 1 22.57 ? C3D HEM 144 A 1 HETATM 32 C C4D HEM . . . D 3 -16.859 20.43 -19.319 1 19.03 ? C4D HEM 144 A 1 HETATM 33 C CMD HEM . . . D 3 -18.363 18.019 -21.937 1 17.43 ? CMD HEM 144 A 1 HETATM 34 C CAD HEM . . . D 3 -16.505 20.919 -21.899 1 16.84 ? CAD HEM 144 A 1 HETATM 35 C CBD HEM . . . D 3 -17.524 21.468 -22.87 1 27.79 ? CBD HEM 144 A 1 HETATM 36 C CGD HEM . . . D 3 -16.708 21.934 -24.041 1 26.96 ? CGD HEM 144 A 1 HETATM 37 O O1D HEM . . . D 3 -16.604 21.174 -25.029 1 23.92 ? O1D HEM 144 A 1 HETATM 38 O O2D HEM . . . D 3 -16.149 23.056 -23.974 1 31.28 ? O2D HEM 144 A 1 HETATM 39 N NA HEM . . . D 3 -15.743 20.877 -16.548 1 19.22 ? NA HEM 144 A 1 HETATM 40 N NB HEM . . . D 3 -16.559 19.046 -14.477 1 18.49 ? NB HEM 144 A 1 HETATM 41 N NC HEM . . . D 3 -18.249 17.613 -16.391 1 19.89 ? NC HEM 144 A 1 HETATM 42 N ND HEM . . . D 3 -17.473 19.459 -18.537 1 19.25 ? ND HEM 144 A 1 HETATM 43 FE FE HEM . . . D 3 -17.015 19.209 -16.507 1 17.98 ? FE HEM 144 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #