data_6KBH # _model_server_result.job_id zXGEER_Qo-2V5JNqFpYaqQ _model_server_result.datetime_utc '2024-10-19 21:46:08' _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 6kbh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":802}' # _entry.id 6KBH # _exptl.entry_id 6KBH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 98.12 _cell.angle_gamma 90 _cell.entry_id 6KBH _cell.length_a 131.762 _cell.length_b 55.484 _cell.length_c 135.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KBH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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,E _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 3 _struct_asym.id C _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 393 1_555 C FE HEM . A HEM 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 A SG CYS 735 A CYS 735 1_555 D FE1 FES . A FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc3 A SG CYS 740 A CYS 740 1_555 D FE1 FES . A FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc4 A SG CYS 743 A CYS 743 1_555 D FE2 FES . A FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc5 A SG CYS 773 A CYS 773 1_555 D FE2 FES . A FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? # _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 187 n n CHA C4D HEM doub 188 n n CHA HHA HEM sing 189 n n CHB C4A HEM sing 190 n n CHB C1B HEM doub 191 n n CHB HHB HEM sing 192 n n CHC C4B HEM sing 193 n n CHC C1C HEM doub 194 n n CHC HHC HEM sing 195 n n CHD C4C HEM doub 196 n n CHD C1D HEM sing 197 n n CHD HHD HEM sing 198 n n C1A C2A HEM doub 199 n y C1A NA HEM sing 200 n y C2A C3A HEM sing 201 n y C2A CAA HEM sing 202 n n C3A C4A HEM doub 203 n y C3A CMA HEM sing 204 n n C4A NA HEM sing 205 n y CMA HMA HEM sing 206 n n CMA HMAA HEM sing 207 n n CMA HMAB HEM sing 208 n n CAA CBA HEM sing 209 n n CAA HAA HEM sing 210 n n CAA HAAA HEM sing 211 n n CBA CGA HEM sing 212 n n CBA HBA HEM sing 213 n n CBA HBAA HEM sing 214 n n CGA O1A HEM doub 215 n n CGA O2A HEM sing 216 n n C1B C2B HEM sing 217 n n C1B NB HEM sing 218 n n C2B C3B HEM doub 219 n n C2B CMB HEM sing 220 n n C3B C4B HEM sing 221 n n C3B CAB HEM sing 222 n n C4B NB HEM doub 223 n n CMB HMB HEM sing 224 n n CMB HMBA HEM sing 225 n n CMB HMBB HEM sing 226 n n CAB CBB HEM doub 227 n n CAB HAB HEM sing 228 n n CBB HBB HEM sing 229 n n CBB HBBA HEM sing 230 n n C1C C2C HEM sing 231 n y C1C NC HEM sing 232 n y C2C C3C HEM doub 233 n y C2C CMC HEM sing 234 n n C3C C4C HEM sing 235 n y C3C CAC HEM sing 236 n n C4C NC HEM sing 237 n y CMC HMC HEM sing 238 n n CMC HMCA HEM sing 239 n n CMC HMCB HEM sing 240 n n CAC CBC HEM doub 241 n n CAC HAC HEM sing 242 n n CBC HBC HEM sing 243 n n CBC HBCA HEM sing 244 n n C1D C2D HEM sing 245 n n C1D ND HEM doub 246 n n C2D C3D HEM doub 247 n n C2D CMD HEM sing 248 n n C3D C4D HEM sing 249 n n C3D CAD HEM sing 250 n n C4D ND HEM sing 251 n n CMD HMD HEM sing 252 n n CMD HMDA HEM sing 253 n n CMD HMDB HEM sing 254 n n CAD CBD HEM sing 255 n n CAD HAD HEM sing 256 n n CAD HADA HEM sing 257 n n CBD CGD HEM sing 258 n n CBD HBD HEM sing 259 n n CBD HBDA HEM sing 260 n n CGD O1D HEM doub 261 n n CGD O2D HEM sing 262 n n O2A H2A HEM sing 263 n n O2D H2D HEM sing 264 n n FE NA HEM sing 265 n n FE NB HEM sing 266 n n FE NC HEM sing 267 n n FE ND HEM sing 268 n n # _atom_sites.entry_id 6KBH _atom_sites.fract_transf_matrix[1][1] 0.007589 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001083 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018023 _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] 0.00743 _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 FMN A 1 801 790 FMN FMN . C 3 HEM A 1 802 791 HEM HEM . D 4 FES A 1 803 792 FES FES . E 5 HOH A 1 901 802 HOH HOH . E 5 HOH A 2 902 804 HOH HOH . E 5 HOH A 3 903 805 HOH HOH . E 5 HOH A 4 904 801 HOH HOH . E 5 HOH A 5 905 803 HOH HOH . E 5 HOH A 6 906 793 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 . . . C 3 -18.701 -34.46 21.73 1 72.55 ? CHA HEM 802 A 1 HETATM 2 C CHB HEM . . . C 3 -14.408 -32.124 22.979 1 63.93 ? CHB HEM 802 A 1 HETATM 3 C CHC HEM . . . C 3 -13.756 -35.399 27.085 1 71.37 ? CHC HEM 802 A 1 HETATM 4 C CHD HEM . . . C 3 -18.018 -37.688 25.818 1 75.61 ? CHD HEM 802 A 1 HETATM 5 C C1A HEM . . . C 3 -17.491 -33.66 21.929 1 72.69 ? C1A HEM 802 A 1 HETATM 6 C C2A HEM . . . C 3 -17.356 -32.615 20.908 1 58.52 ? C2A HEM 802 A 1 HETATM 7 C C3A HEM . . . C 3 -16.17 -31.964 21.255 1 62.31 ? C3A HEM 802 A 1 HETATM 8 C C4A HEM . . . C 3 -15.69 -32.687 22.462 1 54.12 ? C4A HEM 802 A 1 HETATM 9 C CMA HEM . . . C 3 -15.539 -30.804 20.55 1 59.17 ? CMA HEM 802 A 1 HETATM 10 C CAA HEM . . . C 3 -18.272 -32.283 19.77 1 61.54 ? CAA HEM 802 A 1 HETATM 11 C CBA HEM . . . C 3 -19.098 -31.051 19.971 1 63.91 ? CBA HEM 802 A 1 HETATM 12 C CGA HEM . . . C 3 -20.205 -30.746 19.019 1 66.22 ? CGA HEM 802 A 1 HETATM 13 O O1A HEM . . . C 3 -20.057 -31.424 17.968 1 78.76 ? O1A HEM 802 A 1 HETATM 14 O O2A HEM . . . C 3 -20.98 -29.892 19.53 1 62.93 ? O2A HEM 802 A 1 HETATM 15 C C1B HEM . . . C 3 -13.808 -32.769 24.189 1 62.92 ? C1B HEM 802 A 1 HETATM 16 C C2B HEM . . . C 3 -12.505 -32.325 24.867 1 72.66 ? C2B HEM 802 A 1 HETATM 17 C C3B HEM . . . C 3 -12.31 -33.352 26.153 1 59.53 ? C3B HEM 802 A 1 HETATM 18 C C4B HEM . . . C 3 -13.499 -34.292 26.1 1 64.04 ? C4B HEM 802 A 1 HETATM 19 C CMB HEM . . . C 3 -11.609 -31.21 24.447 1 76.81 ? CMB HEM 802 A 1 HETATM 20 C CAB HEM . . . C 3 -11.199 -33.377 27.146 1 62.85 ? CAB HEM 802 A 1 HETATM 21 C CBB HEM . . . C 3 -10.856 -32.108 27.846 1 68.12 ? CBB HEM 802 A 1 HETATM 22 C C1C HEM . . . C 3 -15 -36.183 26.84 1 75.7 ? C1C HEM 802 A 1 HETATM 23 C C2C HEM . . . C 3 -15.122 -37.21 27.841 1 69.59 ? C2C HEM 802 A 1 HETATM 24 C C3C HEM . . . C 3 -16.29 -37.861 27.512 1 74.99 ? C3C HEM 802 A 1 HETATM 25 C C4C HEM . . . C 3 -16.763 -37.148 26.335 1 70.29 ? C4C HEM 802 A 1 HETATM 26 C CMC HEM . . . C 3 -14.199 -37.501 28.978 1 69.16 ? CMC HEM 802 A 1 HETATM 27 C CAC HEM . . . C 3 -16.911 -39.012 28.242 1 78.89 ? CAC HEM 802 A 1 HETATM 28 C CBC HEM . . . C 3 -16.898 -40.378 27.656 1 75.69 ? CBC HEM 802 A 1 HETATM 29 C C1D HEM . . . C 3 -18.403 -36.909 24.635 1 63.44 ? C1D HEM 802 A 1 HETATM 30 C C2D HEM . . . C 3 -19.689 -37.392 24.032 1 60.68 ? C2D HEM 802 A 1 HETATM 31 C C3D HEM . . . C 3 -19.91 -36.383 22.745 1 66.16 ? C3D HEM 802 A 1 HETATM 32 C C4D HEM . . . C 3 -18.718 -35.471 22.806 1 67.02 ? C4D HEM 802 A 1 HETATM 33 C CMD HEM . . . C 3 -20.537 -38.52 24.506 1 76.36 ? CMD HEM 802 A 1 HETATM 34 C CAD HEM . . . C 3 -21.041 -36.387 21.779 1 75.64 ? CAD HEM 802 A 1 HETATM 35 C CBD HEM . . . C 3 -22.307 -35.763 22.268 1 59.85 ? CBD HEM 802 A 1 HETATM 36 C CGD HEM . . . C 3 -23.303 -35.362 21.242 1 68.09 ? CGD HEM 802 A 1 HETATM 37 O O1D HEM . . . C 3 -22.716 -35.304 20.135 1 73.85 ? O1D HEM 802 A 1 HETATM 38 O O2D HEM . . . C 3 -24.433 -35.183 21.764 1 65.26 ? O2D HEM 802 A 1 HETATM 39 N NA HEM . . . C 3 -16.478 -33.729 22.893 1 70.35 ? NA HEM 802 A 1 HETATM 40 N NB HEM . . . C 3 -14.442 -33.893 24.959 1 67.37 ? NB HEM 802 A 1 HETATM 41 N NC HEM . . . C 3 -16.002 -36.124 25.898 1 75.22 ? NC HEM 802 A 1 HETATM 42 N ND HEM . . . C 3 -17.731 -35.694 23.986 1 64.76 ? ND HEM 802 A 1 HETATM 43 FE FE HEM . . . C 3 -15.977 -34.876 24.395 1 75.7 ? FE HEM 802 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #