data_4NKX # _model_server_result.job_id P0jeIt2fAJXnVs4KzMyuog _model_server_result.datetime_utc '2024-11-24 23:27:52' _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 4nkx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 4NKX # _exptl.entry_id 4NKX _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 4 _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 4NKX _cell.length_a 85.934 _cell.length_b 153.036 _cell.length_c 173.243 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NKX _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,M 1 1 B,G,H,N 2 1 C,I,J,O 3 1 D,K,L,P 4 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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 424 A CYS 442 1_555 E FE HEM . A HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc2 B SG CYS 424 B CYS 442 1_555 G FE HEM . B HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc3 C SG CYS 424 C CYS 442 1_555 I FE HEM . C HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc4 D SG CYS 424 D CYS 442 1_555 K FE HEM . D HEM 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? # _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 4NKX _atom_sites.fract_transf_matrix[1][1] 0.011637 _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] 0.006534 _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] 0.005772 _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 E 2 HEM A 1 600 600 HEM HEM . F 3 STR A 1 601 601 STR STR . G 2 HEM B 1 600 600 HEM HEM . H 3 STR B 1 601 601 STR STR . I 2 HEM C 1 600 600 HEM HEM . J 3 STR C 1 601 601 STR STR . K 2 HEM D 1 600 600 HEM HEM . L 3 STR D 1 601 601 STR STR . M 4 HOH A 1 701 1 HOH HOH . M 4 HOH A 2 702 2 HOH HOH . M 4 HOH A 3 703 4 HOH HOH . M 4 HOH A 4 704 5 HOH HOH . M 4 HOH A 5 705 8 HOH HOH . M 4 HOH A 6 706 41 HOH HOH . M 4 HOH A 7 707 46 HOH HOH . M 4 HOH A 8 708 51 HOH HOH . M 4 HOH A 9 709 52 HOH HOH . M 4 HOH A 10 710 64 HOH HOH . M 4 HOH A 11 711 79 HOH HOH . M 4 HOH A 12 712 97 HOH HOH . M 4 HOH A 13 713 98 HOH HOH . M 4 HOH A 14 714 99 HOH HOH . N 4 HOH B 1 701 12 HOH HOH . N 4 HOH B 2 702 13 HOH HOH . N 4 HOH B 3 703 14 HOH HOH . N 4 HOH B 4 704 15 HOH HOH . N 4 HOH B 5 705 21 HOH HOH . N 4 HOH B 6 706 43 HOH HOH . N 4 HOH B 7 707 45 HOH HOH . N 4 HOH B 8 708 50 HOH HOH . N 4 HOH B 9 709 69 HOH HOH . N 4 HOH B 10 710 74 HOH HOH . N 4 HOH B 11 711 80 HOH HOH . N 4 HOH B 12 712 85 HOH HOH . N 4 HOH B 13 713 93 HOH HOH . O 4 HOH C 1 701 22 HOH HOH . O 4 HOH C 2 702 23 HOH HOH . O 4 HOH C 3 703 26 HOH HOH . O 4 HOH C 4 704 28 HOH HOH . O 4 HOH C 5 705 56 HOH HOH . O 4 HOH C 6 706 75 HOH HOH . O 4 HOH C 7 707 82 HOH HOH . O 4 HOH C 8 708 94 HOH HOH . O 4 HOH C 9 709 100 HOH HOH . O 4 HOH C 10 710 101 HOH HOH . P 4 HOH D 1 701 30 HOH HOH . P 4 HOH D 2 702 32 HOH HOH . P 4 HOH D 3 703 35 HOH HOH . P 4 HOH D 4 704 38 HOH HOH . P 4 HOH D 5 705 57 HOH HOH . P 4 HOH D 6 706 90 HOH HOH . P 4 HOH D 7 707 91 HOH HOH . P 4 HOH D 8 708 95 HOH HOH . P 4 HOH D 9 709 102 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 . . . K 2 13.441 20.871 -22.019 1 36.74 ? CHA HEM 600 D 1 HETATM 2 C CHB HEM . . . K 2 12.032 21.534 -17.455 1 37.98 ? CHB HEM 600 D 1 HETATM 3 C CHC HEM . . . K 2 11.56 26.283 -18.268 1 40.44 ? CHC HEM 600 D 1 HETATM 4 C CHD HEM . . . K 2 13.124 25.711 -22.798 1 49.16 ? CHD HEM 600 D 1 HETATM 5 C C1A HEM . . . K 2 13.059 20.629 -20.726 1 37.24 ? C1A HEM 600 D 1 HETATM 6 C C2A HEM . . . K 2 12.901 19.326 -20.128 1 41.42 ? C2A HEM 600 D 1 HETATM 7 C C3A HEM . . . K 2 12.497 19.501 -18.867 1 42.09 ? C3A HEM 600 D 1 HETATM 8 C C4A HEM . . . K 2 12.404 20.923 -18.623 1 37.71 ? C4A HEM 600 D 1 HETATM 9 C CMA HEM . . . K 2 12.195 18.383 -17.845 1 40.52 ? CMA HEM 600 D 1 HETATM 10 C CAA HEM . . . K 2 13.122 17.989 -20.883 1 42.1 ? CAA HEM 600 D 1 HETATM 11 C CBA HEM . . . K 2 14.303 17.188 -20.356 1 31.82 ? CBA HEM 600 D 1 HETATM 12 C CGA HEM . . . K 2 14.417 15.909 -21.152 1 39.28 ? CGA HEM 600 D 1 HETATM 13 O O1A HEM . . . K 2 15.013 14.941 -20.628 1 44.24 ? O1A HEM 600 D 1 HETATM 14 O O2A HEM . . . K 2 13.909 15.831 -22.3 1 39.08 ? O2A HEM 600 D 1 HETATM 15 C C1B HEM . . . K 2 11.787 22.874 -17.293 1 37.42 ? C1B HEM 600 D 1 HETATM 16 C C2B HEM . . . K 2 11.343 23.483 -16.066 1 40.88 ? C2B HEM 600 D 1 HETATM 17 C C3B HEM . . . K 2 11.212 24.808 -16.29 1 40.03 ? C3B HEM 600 D 1 HETATM 18 C C4B HEM . . . K 2 11.571 25.054 -17.665 1 38.63 ? C4B HEM 600 D 1 HETATM 19 C CMB HEM . . . K 2 11.115 22.638 -14.793 1 35.84 ? CMB HEM 600 D 1 HETATM 20 C CAB HEM . . . K 2 10.76 25.979 -15.381 1 39.29 ? CAB HEM 600 D 1 HETATM 21 C CBB HEM . . . K 2 10.209 25.833 -14.173 1 46.35 ? CBB HEM 600 D 1 HETATM 22 C C1C HEM . . . K 2 11.997 26.562 -19.529 1 38.96 ? C1C HEM 600 D 1 HETATM 23 C C2C HEM . . . K 2 12.147 27.877 -20.094 1 45.48 ? C2C HEM 600 D 1 HETATM 24 C C3C HEM . . . K 2 12.596 27.745 -21.345 1 46.54 ? C3C HEM 600 D 1 HETATM 25 C C4C HEM . . . K 2 12.722 26.32 -21.62 1 45.24 ? C4C HEM 600 D 1 HETATM 26 C CMC HEM . . . K 2 11.868 29.201 -19.347 1 41.94 ? CMC HEM 600 D 1 HETATM 27 C CAC HEM . . . K 2 12.888 28.94 -22.289 1 50.43 ? CAC HEM 600 D 1 HETATM 28 C CBC HEM . . . K 2 13.61 28.81 -23.415 1 51.87 ? CBC HEM 600 D 1 HETATM 29 C C1D HEM . . . K 2 13.297 24.351 -23.015 1 46.58 ? C1D HEM 600 D 1 HETATM 30 C C2D HEM . . . K 2 13.63 23.762 -24.294 1 38.37 ? C2D HEM 600 D 1 HETATM 31 C C3D HEM . . . K 2 13.734 22.26 -24.043 1 33.94 ? C3D HEM 600 D 1 HETATM 32 C C4D HEM . . . K 2 13.455 22.091 -22.643 1 35.55 ? C4D HEM 600 D 1 HETATM 33 C CMD HEM . . . K 2 13.82 24.487 -25.633 1 36.34 ? CMD HEM 600 D 1 HETATM 34 C CAD HEM . . . K 2 14.055 21.146 -25.055 1 37.22 ? CAD HEM 600 D 1 HETATM 35 C CBD HEM . . . K 2 15.569 20.997 -25.205 1 37.24 ? CBD HEM 600 D 1 HETATM 36 C CGD HEM . . . K 2 15.894 19.783 -26.046 1 32.49 ? CGD HEM 600 D 1 HETATM 37 O O1D HEM . . . K 2 15.04 18.862 -26.136 1 32.51 ? O1D HEM 600 D 1 HETATM 38 O O2D HEM . . . K 2 17.005 19.745 -26.637 1 29.39 ? O2D HEM 600 D 1 HETATM 39 N NA HEM . . . K 2 12.767 21.58 -19.776 1 42.09 ? NA HEM 600 D 1 HETATM 40 N NB HEM . . . K 2 11.92 23.858 -18.244 1 36.06 ? NB HEM 600 D 1 HETATM 41 N NC HEM . . . K 2 12.354 25.638 -20.477 1 47.67 ? NC HEM 600 D 1 HETATM 42 N ND HEM . . . K 2 13.206 23.332 -22.064 1 36.18 ? ND HEM 600 D 1 HETATM 43 FE FE HEM . . . K 2 12.74 23.636 -20.072 1 33.43 ? FE HEM 600 D 1 HETATM 44 H HHB HEM . . . K 2 11.861 20.954 -16.684 1 45.57 ? HHB HEM 600 D 1 HETATM 45 H HHC HEM . . . K 2 11.204 27.032 -17.745 1 48.53 ? HHC HEM 600 D 1 HETATM 46 H HHD HEM . . . K 2 13.304 26.302 -23.558 1 58.99 ? HHD HEM 600 D 1 HETATM 47 H HMA HEM . . . K 2 11.475 17.813 -18.187 1 48.62 ? HMA HEM 600 D 1 HETATM 48 H HMAA HEM . . . K 2 11.917 18.784 -16.994 1 48.62 ? HMAA HEM 600 D 1 HETATM 49 H HMAB HEM . . . K 2 13 17.842 -17.704 1 48.62 ? HMAB HEM 600 D 1 HETATM 50 H HAA HEM . . . K 2 13.273 18.184 -21.822 1 50.52 ? HAA HEM 600 D 1 HETATM 51 H HAAA HEM . . . K 2 12.32 17.45 -20.802 1 50.52 ? HAAA HEM 600 D 1 HETATM 52 H HBA HEM . . . K 2 14.161 16.977 -19.419 1 38.19 ? HBA HEM 600 D 1 HETATM 53 H HBAA HEM . . . K 2 15.117 17.706 -20.453 1 38.19 ? HBAA HEM 600 D 1 HETATM 54 H HMB HEM . . . K 2 10.439 21.965 -14.968 1 43.01 ? HMB HEM 600 D 1 HETATM 55 H HMBA HEM . . . K 2 10.82 23.214 -14.071 1 43.01 ? HMBA HEM 600 D 1 HETATM 56 H HMBB HEM . . . K 2 11.945 22.203 -14.541 1 43.01 ? HMBB HEM 600 D 1 HETATM 57 H HAB HEM . . . K 2 10.885 26.872 -15.71 1 47.14 ? HAB HEM 600 D 1 HETATM 58 H HBB HEM . . . K 2 9.954 26.615 -13.658 1 55.62 ? HBB HEM 600 D 1 HETATM 59 H HBBA HEM . . . K 2 10.067 24.945 -13.808 1 55.62 ? HBBA HEM 600 D 1 HETATM 60 H HMC HEM . . . K 2 10.941 29.223 -19.063 1 50.32 ? HMC HEM 600 D 1 HETATM 61 H HMCA HEM . . . K 2 12.042 29.949 -19.94 1 50.32 ? HMCA HEM 600 D 1 HETATM 62 H HMCB HEM . . . K 2 12.446 29.262 -18.571 1 50.32 ? HMCB HEM 600 D 1 HETATM 63 H HAC HEM . . . K 2 12.539 29.805 -22.061 1 60.51 ? HAC HEM 600 D 1 HETATM 64 H HBC HEM . . . K 2 13.775 29.582 -23.978 1 62.25 ? HBC HEM 600 D 1 HETATM 65 H HBCA HEM . . . K 2 13.971 27.944 -23.662 1 62.25 ? HBCA HEM 600 D 1 HETATM 66 H HMD HEM . . . K 2 14.041 23.834 -26.329 1 43.61 ? HMD HEM 600 D 1 HETATM 67 H HMDA HEM . . . K 2 14.549 25.136 -25.552 1 43.61 ? HMDA HEM 600 D 1 HETATM 68 H HMDB HEM . . . K 2 12.992 24.953 -25.872 1 43.61 ? HMDB HEM 600 D 1 HETATM 69 H HAD HEM . . . K 2 13.667 21.37 -25.915 1 44.66 ? HAD HEM 600 D 1 HETATM 70 H HADA HEM . . . K 2 13.679 20.308 -24.741 1 44.66 ? HADA HEM 600 D 1 HETATM 71 H HBD HEM . . . K 2 15.97 20.896 -24.328 1 44.69 ? HBD HEM 600 D 1 HETATM 72 H HBDA HEM . . . K 2 15.928 21.79 -25.633 1 44.69 ? HBDA HEM 600 D 1 HETATM 73 H HHA HEM . . . K 2 13.731 20.098 -22.548 1 44.09 ? HHA HEM 600 D 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 73 #