data_7RYB # _model_server_result.job_id wYjfcj8V5aQQb8x9V9JsaQ _model_server_result.datetime_utc '2024-11-30 03:41:55' _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 7ryb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 7RYB # _exptl.entry_id 7RYB _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 99.79 _cell.angle_gamma 90 _cell.entry_id 7RYB _cell.length_a 79.18 _cell.length_b 67.3 _cell.length_c 81.33 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RYB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 470 A CYS 470 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N8 VOR . A VOR 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? # _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 7RYB _atom_sites.fract_transf_matrix[1][1] 0.012629 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002179 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014859 _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] 0.012477 _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 1 601 601 HEM HEM . C 3 VOR A 1 602 602 VOR VOR . D 4 HOH A 1 701 1 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 27.216 8.53 18.369 1 41 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 26.654 11.618 22.183 1 39.05 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 29.122 14.969 19.635 1 44.21 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 29.771 11.886 16.018 1 43.56 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 26.858 9.073 19.588 1 46.53 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 26.107 8.383 20.614 1 40.99 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 25.946 9.217 21.647 1 38.25 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 26.595 10.486 21.353 1 42.78 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 25.188 8.891 22.946 1 37.99 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 25.573 6.942 20.502 1 39.02 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 24.368 6.874 19.568 1 43 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 23.625 5.606 19.914 1 46.76 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 22.52 5.329 19.366 1 48.88 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 24.162 4.86 20.769 1 49.77 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 27.298 12.803 21.851 1 40.29 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 27.496 14.006 22.656 1 40.05 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 28.176 14.903 21.89 1 40.52 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 28.438 14.299 20.625 1 40.99 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 26.992 14.205 24.113 1 39.21 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 28.697 16.354 22.1 1 40.09 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 28.489 17.078 23.201 1 42.52 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 29.549 14.433 18.455 1 45.13 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 30.405 15.102 17.504 1 44.83 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 30.575 14.244 16.475 1 44.83 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 29.852 13.021 16.785 1 42.04 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 30.943 16.534 17.729 1 34.53 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 31.425 14.419 15.196 1 45.33 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 32.547 15.148 15.201 1 46.52 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 29.176 10.697 16.39 1 44.3 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 29.314 9.482 15.645 1 44.93 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 28.616 8.526 16.273 1 41.7 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 28.009 9.124 17.439 1 35.98 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 30.137 9.403 14.34 1 40.06 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 28.48 7.063 15.808 1 38.74 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 27.009 6.701 15.691 1 38.11 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 26.959 5.23 15.427 1 39.4 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 28.042 4.591 15.297 1 35.67 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 25.823 4.71 15.355 1 40.8 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 27.138 10.349 20.071 1 45.47 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 27.894 13.033 20.616 1 42.15 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 29.229 13.176 17.998 1 42.08 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 28.37 10.442 17.488 1 40.47 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 28.22 11.753 19.11 1 35.31 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #