data_1JDL # _model_server_result.job_id 8uchjD902OOuC-CpesOZSg _model_server_result.datetime_utc '2025-02-26 23:06:34' _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 1jdl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 1JDL # _exptl.entry_id 1JDL _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 1JDL _cell.length_a 29.7 _cell.length_b 59.9 _cell.length_c 65.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JDL _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _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 # 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 19 A HIS 19 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 A SD MET 98 A MET 98 1_555 B FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 1JDL _atom_sites.fract_transf_matrix[1][1] 0.03367 _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] 0.016694 _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] 0.015291 _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 1 500 500 HEM HEM . C 3 HOH A 1 1000 1000 HOH TIP . C 3 HOH A 2 1001 1001 HOH TIP . C 3 HOH A 3 1002 1002 HOH TIP . C 3 HOH A 4 1003 1003 HOH TIP . C 3 HOH A 5 1004 1004 HOH TIP . C 3 HOH A 6 1005 1005 HOH TIP . C 3 HOH A 7 1006 1006 HOH TIP . C 3 HOH A 8 1007 1007 HOH TIP . C 3 HOH A 9 1008 1008 HOH TIP . C 3 HOH A 10 1009 1009 HOH TIP . C 3 HOH A 11 1010 1010 HOH TIP . C 3 HOH A 12 1011 1011 HOH TIP . C 3 HOH A 13 1012 1012 HOH TIP . C 3 HOH A 14 1013 1013 HOH TIP . C 3 HOH A 15 1014 1014 HOH TIP . C 3 HOH A 16 1015 1015 HOH TIP . C 3 HOH A 17 1016 1016 HOH TIP . C 3 HOH A 18 1017 1017 HOH TIP . C 3 HOH A 19 1018 1018 HOH TIP . C 3 HOH A 20 1019 1019 HOH TIP . C 3 HOH A 21 1020 1020 HOH TIP . C 3 HOH A 22 1021 1021 HOH TIP . C 3 HOH A 23 1022 1022 HOH TIP . C 3 HOH A 24 1023 1023 HOH TIP . C 3 HOH A 25 1024 1024 HOH TIP . C 3 HOH A 26 1025 1025 HOH TIP . C 3 HOH A 27 1026 1026 HOH TIP . C 3 HOH A 28 1027 1027 HOH TIP . C 3 HOH A 29 1028 1028 HOH TIP . C 3 HOH A 30 1029 1029 HOH TIP . C 3 HOH A 31 1030 1030 HOH TIP . C 3 HOH A 32 1031 1031 HOH TIP . C 3 HOH A 33 1032 1032 HOH TIP . C 3 HOH A 34 1033 1033 HOH TIP . C 3 HOH A 35 1034 1034 HOH TIP . C 3 HOH A 36 1035 1035 HOH TIP . C 3 HOH A 37 1036 1036 HOH TIP . C 3 HOH A 38 1037 1037 HOH TIP . C 3 HOH A 39 1038 1038 HOH TIP . C 3 HOH A 40 1039 1039 HOH TIP . C 3 HOH A 41 1040 1040 HOH TIP . C 3 HOH A 42 1041 1041 HOH TIP . C 3 HOH A 43 1042 1042 HOH TIP . C 3 HOH A 44 1043 1043 HOH TIP . C 3 HOH A 45 1044 1044 HOH TIP . C 3 HOH A 46 1045 1045 HOH TIP . C 3 HOH A 47 1046 1046 HOH TIP . C 3 HOH A 48 1047 1047 HOH TIP . C 3 HOH A 49 1048 1048 HOH TIP . C 3 HOH A 50 1049 1049 HOH TIP . C 3 HOH A 51 1050 1050 HOH TIP . C 3 HOH A 52 1051 1051 HOH TIP . C 3 HOH A 53 1052 1052 HOH TIP . C 3 HOH A 54 1053 1053 HOH TIP . C 3 HOH A 55 1054 1054 HOH TIP . C 3 HOH A 56 1055 1055 HOH TIP . C 3 HOH A 57 1056 1056 HOH TIP . C 3 HOH A 58 1057 1057 HOH TIP . C 3 HOH A 59 1058 1058 HOH TIP . C 3 HOH A 60 1059 1059 HOH TIP . C 3 HOH A 61 1060 1060 HOH TIP . C 3 HOH A 62 1061 1061 HOH TIP . C 3 HOH A 63 1062 1062 HOH TIP . C 3 HOH A 64 1063 1063 HOH TIP . C 3 HOH A 65 1064 1064 HOH TIP . C 3 HOH A 66 1065 1065 HOH TIP . C 3 HOH A 67 1066 1066 HOH TIP . C 3 HOH A 68 1067 1067 HOH TIP . C 3 HOH A 69 1068 1068 HOH TIP . C 3 HOH A 70 1069 1069 HOH TIP . C 3 HOH A 71 1070 1070 HOH TIP . C 3 HOH A 72 1071 1071 HOH TIP . C 3 HOH A 73 1072 1072 HOH TIP . C 3 HOH A 74 1073 1073 HOH TIP . C 3 HOH A 75 1075 1075 HOH TIP . C 3 HOH A 76 1076 1076 HOH TIP . C 3 HOH A 77 1078 1078 HOH TIP . C 3 HOH A 78 1079 1079 HOH TIP . C 3 HOH A 79 1080 1080 HOH TIP . C 3 HOH A 80 1081 1081 HOH TIP . C 3 HOH A 81 1082 1082 HOH TIP . C 3 HOH A 82 1083 1083 HOH TIP . C 3 HOH A 83 1084 1084 HOH TIP . C 3 HOH A 84 1086 1086 HOH TIP . C 3 HOH A 85 1087 1087 HOH TIP . C 3 HOH A 86 1088 1088 HOH TIP . C 3 HOH A 87 1089 1089 HOH TIP . # 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 0.469 6.703 -0.316 1 13.26 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . B 2 2.107 2.325 0.872 1 14.12 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . B 2 6.617 4.059 0.951 1 16.13 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . B 2 4.909 8.49 0.311 1 14.64 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . B 2 0.529 5.333 -0.054 1 14.19 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . B 2 -0.599 4.436 -0.141 1 12.43 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . B 2 -0.122 3.206 0.19 1 12.16 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . B 2 1.282 3.36 0.488 1 14.75 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . B 2 -0.89 1.893 0.194 1 14.35 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . B 2 -2.054 4.856 -0.39 1 13.84 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . B 2 -2.672 5.169 0.972 1 13.78 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . B 2 -4.095 5.731 0.903 1 15.4 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . B 2 -4.685 5.79 -0.194 1 15.99 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . B 2 -4.629 6.109 1.966 1 16.85 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . B 2 3.482 2.435 1.023 1 14.31 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . B 2 4.36 1.342 1.359 1 15.13 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . B 2 5.627 1.809 1.146 1 17.47 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . B 2 5.525 3.205 0.953 1 14.93 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . B 2 3.908 -0.02 1.868 1 15.67 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . B 2 6.819 1.12 0.84 1 22.68 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . B 2 7.02 -0.37 0.624 1 19.03 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . B 2 6.552 5.405 0.736 1 15.27 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . B 2 7.691 6.299 0.727 1 16.79 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . B 2 7.207 7.503 0.38 1 17.82 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . B 2 5.762 7.404 0.427 1 16.12 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . B 2 9.137 5.934 1.069 1 17.67 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . B 2 7.883 8.632 -0.134 1 24.84 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . B 2 9.377 8.909 -0.263 1 23.76 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . B 2 3.543 8.408 0.162 1 13.52 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . B 2 2.696 9.541 -0.128 1 13.61 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . B 2 1.45 9.042 -0.386 1 14.72 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . B 2 1.554 7.588 -0.223 1 13.24 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . B 2 3.117 11.011 -0.209 1 13.82 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . B 2 0.233 9.839 -0.865 1 14.05 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . B 2 0.252 9.794 -2.397 1 16.17 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . B 2 -0.811 10.655 -3.049 1 15.36 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . B 2 -0.833 10.704 -4.298 1 15.41 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . B 2 -1.624 11.279 -2.332 1 16.86 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . B 2 1.685 4.666 0.313 1 13.73 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . B 2 4.197 3.59 0.784 1 14.47 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . B 2 5.367 6.089 0.529 1 14.32 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . B 2 2.848 7.211 0.114 1 13.7 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . B 2 3.539 5.379 0.397 1 14.03 ? FE HEM 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #