data_4NKX # _model_server_result.job_id hw38DzBxoDWK5KmkQjbIrA _model_server_result.datetime_utc '2024-10-12 06:25:33' _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":"E","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 . . . E 2 -27.619 -11.079 -33.471 1 42.32 ? CHA HEM 600 A 1 HETATM 2 C CHB HEM . . . E 2 -26.046 -10.701 -38.021 1 31.23 ? CHB HEM 600 A 1 HETATM 3 C CHC HEM . . . E 2 -29.983 -8.079 -39.149 1 36.65 ? CHC HEM 600 A 1 HETATM 4 C CHD HEM . . . E 2 -31.794 -8.755 -34.701 1 37.29 ? CHD HEM 600 A 1 HETATM 5 C C1A HEM . . . E 2 -26.801 -11.136 -34.581 1 42.68 ? C1A HEM 600 A 1 HETATM 6 C C2A HEM . . . E 2 -25.42 -11.594 -34.603 1 39.26 ? C2A HEM 600 A 1 HETATM 7 C C3A HEM . . . E 2 -24.976 -11.482 -35.86 1 43.28 ? C3A HEM 600 A 1 HETATM 8 C C4A HEM . . . E 2 -26.069 -10.97 -36.674 1 31.9 ? C4A HEM 600 A 1 HETATM 9 C CMA HEM . . . E 2 -23.546 -11.84 -36.355 1 47.11 ? CMA HEM 600 A 1 HETATM 10 C CAA HEM . . . E 2 -24.624 -12.067 -33.363 1 41.93 ? CAA HEM 600 A 1 HETATM 11 C CBA HEM . . . E 2 -24.146 -13.505 -33.495 1 45.02 ? CBA HEM 600 A 1 HETATM 12 C CGA HEM . . . E 2 -23.598 -13.999 -32.168 1 44.81 ? CGA HEM 600 A 1 HETATM 13 O O1A HEM . . . E 2 -23.196 -15.2 -32.11 1 42.16 ? O1A HEM 600 A 1 HETATM 14 O O2A HEM . . . E 2 -23.566 -13.212 -31.173 1 31.66 ? O2A HEM 600 A 1 HETATM 15 C C1B HEM . . . E 2 -26.954 -9.902 -38.699 1 37.39 ? C1B HEM 600 A 1 HETATM 16 C C2B HEM . . . E 2 -26.766 -9.4 -40.049 1 39.68 ? C2B HEM 600 A 1 HETATM 17 C C3B HEM . . . E 2 -27.854 -8.664 -40.36 1 36.08 ? C3B HEM 600 A 1 HETATM 18 C C4B HEM . . . E 2 -28.753 -8.702 -39.221 1 33.69 ? C4B HEM 600 A 1 HETATM 19 C CMB HEM . . . E 2 -25.49 -9.715 -40.878 1 25.95 ? CMB HEM 600 A 1 HETATM 20 C CAB HEM . . . E 2 -28.236 -7.9 -41.651 1 35.93 ? CAB HEM 600 A 1 HETATM 21 C CBB HEM . . . E 2 -27.662 -8.101 -42.842 1 37.69 ? CBB HEM 600 A 1 HETATM 22 C C1C HEM . . . E 2 -30.871 -8.129 -38.093 1 38.14 ? C1C HEM 600 A 1 HETATM 23 C C2C HEM . . . E 2 -32.263 -7.749 -38.136 1 45.96 ? C2C HEM 600 A 1 HETATM 24 C C3C HEM . . . E 2 -32.802 -7.917 -36.919 1 48.53 ? C3C HEM 600 A 1 HETATM 25 C C4C HEM . . . E 2 -31.742 -8.425 -36.048 1 32.09 ? C4C HEM 600 A 1 HETATM 26 C CMC HEM . . . E 2 -33 -7.232 -39.399 1 45.94 ? CMC HEM 600 A 1 HETATM 27 C CAC HEM . . . E 2 -34.306 -7.6 -36.611 1 47.26 ? CAC HEM 600 A 1 HETATM 28 C CBC HEM . . . E 2 -34.882 -7.79 -35.412 1 52.04 ? CBC HEM 600 A 1 HETATM 29 C C1D HEM . . . E 2 -30.816 -9.397 -33.942 1 45.2 ? C1D HEM 600 A 1 HETATM 30 C C2D HEM . . . E 2 -30.907 -9.655 -32.516 1 41.07 ? C2D HEM 600 A 1 HETATM 31 C C3D HEM . . . E 2 -29.611 -10.383 -32.131 1 47.28 ? C3D HEM 600 A 1 HETATM 32 C C4D HEM . . . E 2 -28.859 -10.487 -33.366 1 39.18 ? C4D HEM 600 A 1 HETATM 33 C CMD HEM . . . E 2 -32.059 -9.283 -31.57 1 42.23 ? CMD HEM 600 A 1 HETATM 34 C CAD HEM . . . E 2 -29.192 -10.89 -30.724 1 44.6 ? CAD HEM 600 A 1 HETATM 35 C CBD HEM . . . E 2 -29.191 -12.424 -30.68 1 39.78 ? CBD HEM 600 A 1 HETATM 36 C CGD HEM . . . E 2 -28.996 -12.941 -29.266 1 48.68 ? CGD HEM 600 A 1 HETATM 37 O O1D HEM . . . E 2 -28.272 -12.303 -28.452 1 48.98 ? O1D HEM 600 A 1 HETATM 38 O O2D HEM . . . E 2 -29.577 -14.009 -28.938 1 47.78 ? O2D HEM 600 A 1 HETATM 39 N NA HEM . . . E 2 -27.166 -10.771 -35.859 1 46.73 ? NA HEM 600 A 1 HETATM 40 N NB HEM . . . E 2 -28.176 -9.457 -38.223 1 31.21 ? NB HEM 600 A 1 HETATM 41 N NC HEM . . . E 2 -30.597 -8.532 -36.808 1 39.84 ? NC HEM 600 A 1 HETATM 42 N ND HEM . . . E 2 -29.589 -9.9 -34.39 1 35.71 ? ND HEM 600 A 1 HETATM 43 FE FE HEM . . . E 2 -28.993 -9.825 -36.3 1 37.53 ? FE HEM 600 A 1 HETATM 44 H HHB HEM . . . E 2 -25.266 -11.015 -38.524 1 37.47 ? HHB HEM 600 A 1 HETATM 45 H HHC HEM . . . E 2 -30.253 -7.547 -39.926 1 43.98 ? HHC HEM 600 A 1 HETATM 46 H HHD HEM . . . E 2 -32.615 -8.509 -34.226 1 44.75 ? HHD HEM 600 A 1 HETATM 47 H HMA HEM . . . E 2 -22.888 -11.291 -35.879 1 56.54 ? HMA HEM 600 A 1 HETATM 48 H HMAA HEM . . . E 2 -23.481 -11.667 -37.317 1 56.54 ? HMAA HEM 600 A 1 HETATM 49 H HMAB HEM . . . E 2 -23.368 -12.788 -36.181 1 56.54 ? HMAB HEM 600 A 1 HETATM 50 H HAA HEM . . . E 2 -25.192 -11.996 -32.579 1 50.32 ? HAA HEM 600 A 1 HETATM 51 H HAAA HEM . . . E 2 -23.853 -11.49 -33.245 1 50.32 ? HAAA HEM 600 A 1 HETATM 52 H HBA HEM . . . E 2 -23.449 -13.552 -34.168 1 54.02 ? HBA HEM 600 A 1 HETATM 53 H HBAA HEM . . . E 2 -24.89 -14.067 -33.764 1 54.02 ? HBAA HEM 600 A 1 HETATM 54 H HMB HEM . . . E 2 -24.71 -9.376 -40.412 1 31.14 ? HMB HEM 600 A 1 HETATM 55 H HMBA HEM . . . E 2 -25.557 -9.29 -41.748 1 31.14 ? HMBA HEM 600 A 1 HETATM 56 H HMBB HEM . . . E 2 -25.408 -10.675 -40.992 1 31.14 ? HMBB HEM 600 A 1 HETATM 57 H HAB HEM . . . E 2 -28.93 -7.239 -41.592 1 43.12 ? HAB HEM 600 A 1 HETATM 58 H HBB HEM . . . E 2 -27.947 -7.584 -43.611 1 45.22 ? HBB HEM 600 A 1 HETATM 59 H HBBA HEM . . . E 2 -26.958 -8.761 -42.936 1 45.22 ? HBBA HEM 600 A 1 HETATM 60 H HMC HEM . . . E 2 -32.571 -6.422 -39.714 1 55.13 ? HMC HEM 600 A 1 HETATM 61 H HMCA HEM . . . E 2 -33.925 -7.043 -39.178 1 55.13 ? HMCA HEM 600 A 1 HETATM 62 H HMCB HEM . . . E 2 -32.965 -7.908 -40.093 1 55.13 ? HMCB HEM 600 A 1 HETATM 63 H HAC HEM . . . E 2 -34.848 -7.25 -37.322 1 56.71 ? HAC HEM 600 A 1 HETATM 64 H HBC HEM . . . E 2 -35.82 -7.578 -35.286 1 62.45 ? HBC HEM 600 A 1 HETATM 65 H HBCA HEM . . . E 2 -34.361 -8.143 -34.674 1 62.45 ? HBCA HEM 600 A 1 HETATM 66 H HMD HEM . . . E 2 -31.845 -9.583 -30.662 1 50.68 ? HMD HEM 600 A 1 HETATM 67 H HMDA HEM . . . E 2 -32.883 -9.718 -31.872 1 50.68 ? HMDA HEM 600 A 1 HETATM 68 H HMDB HEM . . . E 2 -32.183 -8.311 -31.573 1 50.68 ? HMDB HEM 600 A 1 HETATM 69 H HAD HEM . . . E 2 -29.816 -10.551 -30.063 1 53.52 ? HAD HEM 600 A 1 HETATM 70 H HADA HEM . . . E 2 -28.302 -10.564 -30.519 1 53.52 ? HADA HEM 600 A 1 HETATM 71 H HBD HEM . . . E 2 -28.473 -12.757 -31.241 1 47.74 ? HBD HEM 600 A 1 HETATM 72 H HBDA HEM . . . E 2 -30.038 -12.751 -31.023 1 47.74 ? HBDA HEM 600 A 1 HETATM 73 H HHA HEM . . . E 2 -27.277 -11.511 -32.66 1 50.78 ? HHA HEM 600 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 73 #