data_6XK8 # _model_server_result.job_id fdvva_xo_RhDRldKEKtPcQ _model_server_result.datetime_utc '2025-01-25 10:55:35' _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 6xk8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 6XK8 # _exptl.entry_id 6XK8 _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 1 _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 6XK8 _cell.length_a 80.599 _cell.length_b 94.499 _cell.length_c 61.929 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XK8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 66 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 66 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 901 _struct_conn.ptnr2_symmetry 1_555 _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 2.562 _struct_conn.pdbx_value_order ? # _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 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 6XK8 _atom_sites.fract_transf_matrix[1][1] 0.012407 _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] 0.010582 _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] 0.016148 _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 B 2 HEM A 1 901 901 HEM HEM . C 3 V54 A 1 902 1 V54 PWA . D 4 CL A 1 903 1 CL CL . E 5 GOL A 1 904 1 GOL GOL . F 5 GOL A 1 905 2 GOL GOL . G 5 GOL A 1 906 3 GOL GOL . H 6 PEG A 1 907 2 PEG PEG . I 7 POL A 1 908 1 POL POL . J 8 HOH A 1 1001 85 HOH HOH . J 8 HOH A 2 1002 99 HOH HOH . J 8 HOH A 3 1003 11 HOH HOH . J 8 HOH A 4 1004 97 HOH HOH . J 8 HOH A 5 1005 12 HOH HOH . J 8 HOH A 6 1006 52 HOH HOH . J 8 HOH A 7 1007 110 HOH HOH . J 8 HOH A 8 1008 43 HOH HOH . J 8 HOH A 9 1009 90 HOH HOH . J 8 HOH A 10 1010 7 HOH HOH . J 8 HOH A 11 1011 39 HOH HOH . J 8 HOH A 12 1012 117 HOH HOH . J 8 HOH A 13 1013 14 HOH HOH . J 8 HOH A 14 1014 124 HOH HOH . J 8 HOH A 15 1015 51 HOH HOH . J 8 HOH A 16 1016 57 HOH HOH . J 8 HOH A 17 1017 53 HOH HOH . J 8 HOH A 18 1018 64 HOH HOH . J 8 HOH A 19 1019 32 HOH HOH . J 8 HOH A 20 1020 59 HOH HOH . J 8 HOH A 21 1021 37 HOH HOH . J 8 HOH A 22 1022 6 HOH HOH . J 8 HOH A 23 1023 58 HOH HOH . J 8 HOH A 24 1024 68 HOH HOH . J 8 HOH A 25 1025 105 HOH HOH . J 8 HOH A 26 1026 1 HOH HOH . J 8 HOH A 27 1027 104 HOH HOH . J 8 HOH A 28 1028 61 HOH HOH . J 8 HOH A 29 1029 67 HOH HOH . J 8 HOH A 30 1030 4 HOH HOH . J 8 HOH A 31 1031 81 HOH HOH . J 8 HOH A 32 1032 25 HOH HOH . J 8 HOH A 33 1033 63 HOH HOH . J 8 HOH A 34 1034 106 HOH HOH . J 8 HOH A 35 1035 15 HOH HOH . J 8 HOH A 36 1036 66 HOH HOH . J 8 HOH A 37 1037 9 HOH HOH . J 8 HOH A 38 1038 34 HOH HOH . J 8 HOH A 39 1039 122 HOH HOH . J 8 HOH A 40 1040 18 HOH HOH . J 8 HOH A 41 1041 8 HOH HOH . J 8 HOH A 42 1042 78 HOH HOH . J 8 HOH A 43 1043 22 HOH HOH . J 8 HOH A 44 1044 27 HOH HOH . J 8 HOH A 45 1045 109 HOH HOH . J 8 HOH A 46 1046 94 HOH HOH . J 8 HOH A 47 1047 55 HOH HOH . J 8 HOH A 48 1048 29 HOH HOH . J 8 HOH A 49 1049 35 HOH HOH . J 8 HOH A 50 1050 49 HOH HOH . J 8 HOH A 51 1051 75 HOH HOH . J 8 HOH A 52 1052 16 HOH HOH . J 8 HOH A 53 1053 30 HOH HOH . J 8 HOH A 54 1054 26 HOH HOH . J 8 HOH A 55 1055 56 HOH HOH . J 8 HOH A 56 1056 23 HOH HOH . J 8 HOH A 57 1057 69 HOH HOH . J 8 HOH A 58 1058 5 HOH HOH . J 8 HOH A 59 1059 42 HOH HOH . J 8 HOH A 60 1060 88 HOH HOH . J 8 HOH A 61 1061 92 HOH HOH . J 8 HOH A 62 1062 47 HOH HOH . J 8 HOH A 63 1063 50 HOH HOH . J 8 HOH A 64 1064 115 HOH HOH . J 8 HOH A 65 1065 24 HOH HOH . J 8 HOH A 66 1066 31 HOH HOH . J 8 HOH A 67 1067 46 HOH HOH . J 8 HOH A 68 1068 103 HOH HOH . J 8 HOH A 69 1069 33 HOH HOH . J 8 HOH A 70 1070 113 HOH HOH . J 8 HOH A 71 1071 3 HOH HOH . J 8 HOH A 72 1072 20 HOH HOH . J 8 HOH A 73 1073 119 HOH HOH . J 8 HOH A 74 1074 107 HOH HOH . J 8 HOH A 75 1075 40 HOH HOH . J 8 HOH A 76 1076 19 HOH HOH . J 8 HOH A 77 1077 91 HOH HOH . J 8 HOH A 78 1078 111 HOH HOH . J 8 HOH A 79 1079 72 HOH HOH . J 8 HOH A 80 1080 13 HOH HOH . J 8 HOH A 81 1081 79 HOH HOH . J 8 HOH A 82 1082 74 HOH HOH . J 8 HOH A 83 1083 21 HOH HOH . J 8 HOH A 84 1084 2 HOH HOH . J 8 HOH A 85 1085 121 HOH HOH . J 8 HOH A 86 1086 108 HOH HOH . J 8 HOH A 87 1087 101 HOH HOH . J 8 HOH A 88 1088 95 HOH HOH . J 8 HOH A 89 1089 36 HOH HOH . J 8 HOH A 90 1090 96 HOH HOH . J 8 HOH A 91 1091 80 HOH HOH . J 8 HOH A 92 1092 83 HOH HOH . J 8 HOH A 93 1093 28 HOH HOH . J 8 HOH A 94 1094 71 HOH HOH . J 8 HOH A 95 1095 70 HOH HOH . J 8 HOH A 96 1096 76 HOH HOH . J 8 HOH A 97 1097 112 HOH HOH . J 8 HOH A 98 1098 102 HOH HOH . J 8 HOH A 99 1099 41 HOH HOH . J 8 HOH A 100 1100 38 HOH HOH . J 8 HOH A 101 1101 84 HOH HOH . J 8 HOH A 102 1102 54 HOH HOH . J 8 HOH A 103 1103 93 HOH HOH . J 8 HOH A 104 1104 87 HOH HOH . J 8 HOH A 105 1105 17 HOH HOH . J 8 HOH A 106 1106 65 HOH HOH . J 8 HOH A 107 1107 89 HOH HOH . J 8 HOH A 108 1108 86 HOH HOH . J 8 HOH A 109 1109 120 HOH HOH . J 8 HOH A 110 1110 114 HOH HOH . J 8 HOH A 111 1111 118 HOH HOH . J 8 HOH A 112 1112 45 HOH HOH . J 8 HOH A 113 1113 82 HOH HOH . J 8 HOH A 114 1114 48 HOH HOH . J 8 HOH A 115 1115 116 HOH HOH . J 8 HOH A 116 1116 123 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 . . . B 2 1.701 14.356 21.039 1 34.25 ? CHA HEM 901 A 1 HETATM 2 C CHB HEM . . . B 2 -0.908 15.486 24.975 1 33.52 ? CHB HEM 901 A 1 HETATM 3 C CHC HEM . . . B 2 -1.349 20.043 23.304 1 32.86 ? CHC HEM 901 A 1 HETATM 4 C CHD HEM . . . B 2 0.649 18.694 19.109 1 35.88 ? CHD HEM 901 A 1 HETATM 5 C C1A HEM . . . B 2 1.126 14.367 22.285 1 33.71 ? C1A HEM 901 A 1 HETATM 6 C C2A HEM . . . B 2 1.342 13.333 23.234 1 35.11 ? C2A HEM 901 A 1 HETATM 7 C C3A HEM . . . B 2 0.614 13.646 24.33 1 35.22 ? C3A HEM 901 A 1 HETATM 8 C C4A HEM . . . B 2 -0.051 14.873 24.077 1 34.84 ? C4A HEM 901 A 1 HETATM 9 C CMA HEM . . . B 2 0.528 12.829 25.596 1 31.68 ? CMA HEM 901 A 1 HETATM 10 C CAA HEM . . . B 2 2.176 12.073 23.076 1 35.4 ? CAA HEM 901 A 1 HETATM 11 C CBA HEM . . . B 2 3.535 12.078 23.795 1 38.45 ? CBA HEM 901 A 1 HETATM 12 C CGA HEM . . . B 2 3.93 10.645 24.149 1 43.17 ? CGA HEM 901 A 1 HETATM 13 O O1A HEM . . . B 2 4.914 10.442 24.904 1 45.34 ? O1A HEM 901 A 1 HETATM 14 O O2A HEM . . . B 2 3.286 9.641 23.714 1 37.35 ? O2A HEM 901 A 1 HETATM 15 C C1B HEM . . . B 2 -1.22 16.842 24.844 1 34.92 ? C1B HEM 901 A 1 HETATM 16 C C2B HEM . . . B 2 -1.843 17.571 25.895 1 34.8 ? C2B HEM 901 A 1 HETATM 17 C C3B HEM . . . B 2 -1.987 18.854 25.468 1 35.73 ? C3B HEM 901 A 1 HETATM 18 C C4B HEM . . . B 2 -1.414 18.881 24.085 1 35.06 ? C4B HEM 901 A 1 HETATM 19 C CMB HEM . . . B 2 -2.272 17.025 27.246 1 34.08 ? CMB HEM 901 A 1 HETATM 20 C CAB HEM . . . B 2 -2.588 19.954 26.27 1 33.79 ? CAB HEM 901 A 1 HETATM 21 C CBB HEM . . . B 2 -3.286 20.962 25.727 1 33.3 ? CBB HEM 901 A 1 HETATM 22 C C1C HEM . . . B 2 -0.777 20.134 22.037 1 33.61 ? C1C HEM 901 A 1 HETATM 23 C C2C HEM . . . B 2 -0.567 21.304 21.282 1 35.79 ? C2C HEM 901 A 1 HETATM 24 C C3C HEM . . . B 2 0.002 20.919 20.064 1 35.62 ? C3C HEM 901 A 1 HETATM 25 C C4C HEM . . . B 2 0.141 19.5 20.105 1 34.48 ? C4C HEM 901 A 1 HETATM 26 C CMC HEM . . . B 2 -0.916 22.704 21.747 1 33.84 ? CMC HEM 901 A 1 HETATM 27 C CAC HEM . . . B 2 0.416 21.779 18.925 1 36.82 ? CAC HEM 901 A 1 HETATM 28 C CBC HEM . . . B 2 -0.191 22.914 18.573 1 35.62 ? CBC HEM 901 A 1 HETATM 29 C C1D HEM . . . B 2 1.109 17.391 19.36 1 35.6 ? C1D HEM 901 A 1 HETATM 30 C C2D HEM . . . B 2 1.968 16.709 18.376 1 33.79 ? C2D HEM 901 A 1 HETATM 31 C C3D HEM . . . B 2 2.273 15.507 18.898 1 32.76 ? C3D HEM 901 A 1 HETATM 32 C C4D HEM . . . B 2 1.606 15.468 20.217 1 34.02 ? C4D HEM 901 A 1 HETATM 33 C CMD HEM . . . B 2 2.406 17.269 17.04 1 33.46 ? CMD HEM 901 A 1 HETATM 34 C CAD HEM . . . B 2 3.14 14.433 18.261 1 34.96 ? CAD HEM 901 A 1 HETATM 35 C CBD HEM . . . B 2 4.641 14.809 18.271 1 36.65 ? CBD HEM 901 A 1 HETATM 36 C CGD HEM . . . B 2 5.495 13.641 17.817 1 37.75 ? CGD HEM 901 A 1 HETATM 37 O O1D HEM . . . B 2 6.598 13.419 18.359 1 37.05 ? O1D HEM 901 A 1 HETATM 38 O O2D HEM . . . B 2 5.115 12.878 16.899 1 38.35 ? O2D HEM 901 A 1 HETATM 39 N NA HEM . . . B 2 0.261 15.321 22.807 1 34.58 ? NA HEM 901 A 1 HETATM 40 N NB HEM . . . B 2 -0.966 17.636 23.798 1 31.57 ? NB HEM 901 A 1 HETATM 41 N NC HEM . . . B 2 -0.355 19.07 21.304 1 35.77 ? NC HEM 901 A 1 HETATM 42 N ND HEM . . . B 2 0.937 16.619 20.457 1 35.38 ? ND HEM 901 A 1 HETATM 43 FE FE HEM . . . B 2 -0.154 17.09 21.934 1 37.99 ? FE HEM 901 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #