data_3K1O # _model_server_result.job_id JbXK4Edti9l6wW9WQDiDOw _model_server_result.datetime_utc '2024-11-27 04:46:29' _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 3k1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":488}' # _entry.id 3K1O # _exptl.entry_id 3K1O _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 120 _cell.entry_id 3K1O _cell.length_a 63.121 _cell.length_b 63.121 _cell.length_c 229.302 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 SG CYS 393 A CYS 422 1_555 B FE HEM . A HEM 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc2 B FE HEM . A HEM 488 1_555 C NBD POZ . A POZ 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _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 3K1O _atom_sites.fract_transf_matrix[1][1] 0.015843 _atom_sites.fract_transf_matrix[1][2] 0.009147 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018293 _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] 0.004361 _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 1 488 488 HEM HEM . C 3 POZ A 1 490 490 POZ POZ . D 4 HOH A 1 1 1 HOH HOH . D 4 HOH A 2 3 3 HOH HOH . D 4 HOH A 3 5 5 HOH HOH . D 4 HOH A 4 7 7 HOH HOH . D 4 HOH A 5 8 8 HOH HOH . D 4 HOH A 6 9 9 HOH HOH . D 4 HOH A 7 11 11 HOH HOH . D 4 HOH A 8 12 12 HOH HOH . D 4 HOH A 9 13 13 HOH HOH . D 4 HOH A 10 14 14 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 -37.515 9.658 -24.397 1 53.95 ? CHA HEM 488 A 1 HETATM 2 C CHB HEM . . . B 2 -36.685 5.365 -22.759 1 49.47 ? CHB HEM 488 A 1 HETATM 3 C CHC HEM . . . B 2 -32.375 6.705 -21.689 1 53.13 ? CHC HEM 488 A 1 HETATM 4 C CHD HEM . . . B 2 -33.483 11.13 -22.502 1 56.83 ? CHD HEM 488 A 1 HETATM 5 C C1A HEM . . . B 2 -37.575 8.386 -24.017 1 51.92 ? C1A HEM 488 A 1 HETATM 6 C C2A HEM . . . B 2 -38.77 7.641 -24.183 1 52.92 ? C2A HEM 488 A 1 HETATM 7 C C3A HEM . . . B 2 -38.519 6.461 -23.733 1 51.94 ? C3A HEM 488 A 1 HETATM 8 C C4A HEM . . . B 2 -37.193 6.463 -23.275 1 51.89 ? C4A HEM 488 A 1 HETATM 9 C CMA HEM . . . B 2 -39.427 5.245 -23.659 1 48.89 ? CMA HEM 488 A 1 HETATM 10 C CAA HEM . . . B 2 -40.079 8.142 -24.796 1 51.06 ? CAA HEM 488 A 1 HETATM 11 C CBA HEM . . . B 2 -40.836 8.981 -23.787 1 61.25 ? CBA HEM 488 A 1 HETATM 12 C CGA HEM . . . B 2 -42.223 9.154 -24.303 1 67.61 ? CGA HEM 488 A 1 HETATM 13 O O1A HEM . . . B 2 -42.452 8.655 -25.406 1 72.66 ? O1A HEM 488 A 1 HETATM 14 O O2A HEM . . . B 2 -43.09 9.765 -23.65 1 66.56 ? O2A HEM 488 A 1 HETATM 15 C C1B HEM . . . B 2 -35.436 5.433 -22.363 1 51.03 ? C1B HEM 488 A 1 HETATM 16 C C2B HEM . . . B 2 -34.755 4.293 -21.884 1 51.23 ? C2B HEM 488 A 1 HETATM 17 C C3B HEM . . . B 2 -33.574 4.672 -21.591 1 52.5 ? C3B HEM 488 A 1 HETATM 18 C C4B HEM . . . B 2 -33.494 6.05 -21.894 1 54.02 ? C4B HEM 488 A 1 HETATM 19 C CMB HEM . . . B 2 -35.273 2.876 -21.723 1 46.16 ? CMB HEM 488 A 1 HETATM 20 C CAB HEM . . . B 2 -32.486 3.776 -21.038 1 52.17 ? CAB HEM 488 A 1 HETATM 21 C CBB HEM . . . B 2 -32.698 2.473 -21.112 1 55.7 ? CBB HEM 488 A 1 HETATM 22 C C1C HEM . . . B 2 -32.384 8.013 -21.819 1 54.63 ? C1C HEM 488 A 1 HETATM 23 C C2C HEM . . . B 2 -31.253 8.794 -21.481 1 53.02 ? C2C HEM 488 A 1 HETATM 24 C C3C HEM . . . B 2 -31.564 10.008 -21.715 1 53.88 ? C3C HEM 488 A 1 HETATM 25 C C4C HEM . . . B 2 -32.895 9.996 -22.176 1 54.9 ? C4C HEM 488 A 1 HETATM 26 C CMC HEM . . . B 2 -29.915 8.293 -20.965 1 50.45 ? CMC HEM 488 A 1 HETATM 27 C CAC HEM . . . B 2 -30.691 11.24 -21.522 1 59.26 ? CAC HEM 488 A 1 HETATM 28 C CBC HEM . . . B 2 -29.488 11.313 -22.084 1 58.71 ? CBC HEM 488 A 1 HETATM 29 C C1D HEM . . . B 2 -34.601 11.067 -23.186 1 56.88 ? C1D HEM 488 A 1 HETATM 30 C C2D HEM . . . B 2 -35.015 12.157 -23.96 1 57.33 ? C2D HEM 488 A 1 HETATM 31 C C3D HEM . . . B 2 -36.291 11.711 -24.564 1 58.08 ? C3D HEM 488 A 1 HETATM 32 C C4D HEM . . . B 2 -36.464 10.398 -24.064 1 57.15 ? C4D HEM 488 A 1 HETATM 33 C CMD HEM . . . B 2 -34.296 13.484 -24.128 1 61.87 ? CMD HEM 488 A 1 HETATM 34 C CAD HEM . . . B 2 -37.177 12.503 -25.516 1 59.68 ? CAD HEM 488 A 1 HETATM 35 C CBD HEM . . . B 2 -38.524 12.755 -24.891 1 65.43 ? CBD HEM 488 A 1 HETATM 36 C CGD HEM . . . B 2 -39.191 13.617 -25.891 1 65.8 ? CGD HEM 488 A 1 HETATM 37 O O1D HEM . . . B 2 -38.588 13.815 -26.945 1 67.88 ? O1D HEM 488 A 1 HETATM 38 O O2D HEM . . . B 2 -40.296 14.098 -25.647 1 66.82 ? O2D HEM 488 A 1 HETATM 39 N NA HEM . . . B 2 -36.567 7.663 -23.438 1 51.68 ? NA HEM 488 A 1 HETATM 40 N NB HEM . . . B 2 -34.657 6.559 -22.381 1 51.34 ? NB HEM 488 A 1 HETATM 41 N NC HEM . . . B 2 -33.437 8.744 -22.255 1 54.44 ? NC HEM 488 A 1 HETATM 42 N ND HEM . . . B 2 -35.448 9.991 -23.236 1 56.16 ? ND HEM 488 A 1 HETATM 43 FE FE HEM . . . B 2 -34.96 8.157 -22.878 1 58.18 ? FE HEM 488 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #