data_4BY0 # _model_server_result.job_id cnJKZxVydklP6Kn75zjuoA _model_server_result.datetime_utc '2024-10-19 11:42:31' _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 4by0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1450}' # _entry.id 4BY0 # _exptl.entry_id 4BY0 _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 2 _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 4BY0 _cell.length_a 124.167 _cell.length_b 124.167 _cell.length_c 119.839 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BY0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 402 A CYS 422 1_555 C FE HEM . A HEM 1450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc2 C FE HEM . A HEM 1450 1_555 D N1 5PS . A 5PS 1460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc3 B SG CYS 402 B CYS 422 1_555 E FE HEM . B HEM 1450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 E FE HEM . B HEM 1450 1_555 F N1 5PS . B 5PS 1460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? # _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 192 n n CHA C4D HEM doub 193 n n CHA HHA HEM sing 194 n n CHB C4A HEM sing 195 n n CHB C1B HEM doub 196 n n CHB HHB HEM sing 197 n n CHC C4B HEM sing 198 n n CHC C1C HEM doub 199 n n CHC HHC HEM sing 200 n n CHD C4C HEM doub 201 n n CHD C1D HEM sing 202 n n CHD HHD HEM sing 203 n n C1A C2A HEM doub 204 n y C1A NA HEM sing 205 n y C2A C3A HEM sing 206 n y C2A CAA HEM sing 207 n n C3A C4A HEM doub 208 n y C3A CMA HEM sing 209 n n C4A NA HEM sing 210 n y CMA HMA HEM sing 211 n n CMA HMAA HEM sing 212 n n CMA HMAB HEM sing 213 n n CAA CBA HEM sing 214 n n CAA HAA HEM sing 215 n n CAA HAAA HEM sing 216 n n CBA CGA HEM sing 217 n n CBA HBA HEM sing 218 n n CBA HBAA HEM sing 219 n n CGA O1A HEM doub 220 n n CGA O2A HEM sing 221 n n C1B C2B HEM sing 222 n n C1B NB HEM sing 223 n n C2B C3B HEM doub 224 n n C2B CMB HEM sing 225 n n C3B C4B HEM sing 226 n n C3B CAB HEM sing 227 n n C4B NB HEM doub 228 n n CMB HMB HEM sing 229 n n CMB HMBA HEM sing 230 n n CMB HMBB HEM sing 231 n n CAB CBB HEM doub 232 n n CAB HAB HEM sing 233 n n CBB HBB HEM sing 234 n n CBB HBBA HEM sing 235 n n C1C C2C HEM sing 236 n y C1C NC HEM sing 237 n y C2C C3C HEM doub 238 n y C2C CMC HEM sing 239 n n C3C C4C HEM sing 240 n y C3C CAC HEM sing 241 n n C4C NC HEM sing 242 n y CMC HMC HEM sing 243 n n CMC HMCA HEM sing 244 n n CMC HMCB HEM sing 245 n n CAC CBC HEM doub 246 n n CAC HAC HEM sing 247 n n CBC HBC HEM sing 248 n n CBC HBCA HEM sing 249 n n C1D C2D HEM sing 250 n n C1D ND HEM doub 251 n n C2D C3D HEM doub 252 n n C2D CMD HEM sing 253 n n C3D C4D HEM sing 254 n n C3D CAD HEM sing 255 n n C4D ND HEM sing 256 n n CMD HMD HEM sing 257 n n CMD HMDA HEM sing 258 n n CMD HMDB HEM sing 259 n n CAD CBD HEM sing 260 n n CAD HAD HEM sing 261 n n CAD HADA HEM sing 262 n n CBD CGD HEM sing 263 n n CBD HBD HEM sing 264 n n CBD HBDA HEM sing 265 n n CGD O1D HEM doub 266 n n CGD O2D HEM sing 267 n n O2A H2A HEM sing 268 n n O2D H2D HEM sing 269 n n FE NA HEM sing 270 n n FE NB HEM sing 271 n n FE NC HEM sing 272 n n FE ND HEM sing 273 n n # _atom_sites.entry_id 4BY0 _atom_sites.fract_transf_matrix[1][1] 0.008054 _atom_sites.fract_transf_matrix[1][2] 0.00465 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0093 _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] 0.008345 _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 C 2 HEM A 1 1450 1450 HEM HEM . D 3 5PS A 1 1460 1460 5PS 5PS . E 2 HEM B 1 1450 1450 HEM HEM . F 3 5PS B 1 1460 1460 5PS 5PS . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 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 2 -54.047 10.762 -4.239 1 49.36 ? CHA HEM 1450 A 1 HETATM 2 C CHB HEM . . . C 2 -55.668 14.706 -6.47 1 44.98 ? CHB HEM 1450 A 1 HETATM 3 C CHC HEM . . . C 2 -58.523 15.523 -2.654 1 43.61 ? CHC HEM 1450 A 1 HETATM 4 C CHD HEM . . . C 2 -56.7 11.809 -0.394 1 42.36 ? CHD HEM 1450 A 1 HETATM 5 C C1A HEM . . . C 2 -54.301 11.733 -5.159 1 49.32 ? C1A HEM 1450 A 1 HETATM 6 C C2A HEM . . . C 2 -53.655 11.806 -6.405 1 51.03 ? C2A HEM 1450 A 1 HETATM 7 C C3A HEM . . . C 2 -54.101 12.907 -7.025 1 46.81 ? C3A HEM 1450 A 1 HETATM 8 C C4A HEM . . . C 2 -55.02 13.532 -6.167 1 45.35 ? C4A HEM 1450 A 1 HETATM 9 C CMA HEM . . . C 2 -53.674 13.362 -8.388 1 46.93 ? CMA HEM 1450 A 1 HETATM 10 C CAA HEM . . . C 2 -52.639 10.817 -6.929 1 53.97 ? CAA HEM 1450 A 1 HETATM 11 C CBA HEM . . . C 2 -51.31 11.154 -6.227 1 53.16 ? CBA HEM 1450 A 1 HETATM 12 C CGA HEM . . . C 2 -50.323 10.034 -6.375 1 51.79 ? CGA HEM 1450 A 1 HETATM 13 O O1A HEM . . . C 2 -50.553 9.139 -7.234 1 48.5 ? O1A HEM 1450 A 1 HETATM 14 O O2A HEM . . . C 2 -49.298 10.036 -5.635 1 47.29 ? O2A HEM 1450 A 1 HETATM 15 C C1B HEM . . . C 2 -56.586 15.283 -5.596 1 46.75 ? C1B HEM 1450 A 1 HETATM 16 C C2B HEM . . . C 2 -57.304 16.468 -5.913 1 48.47 ? C2B HEM 1450 A 1 HETATM 17 C C3B HEM . . . C 2 -58.126 16.701 -4.837 1 50.95 ? C3B HEM 1450 A 1 HETATM 18 C C4B HEM . . . C 2 -57.871 15.61 -3.869 1 45.78 ? C4B HEM 1450 A 1 HETATM 19 C CMB HEM . . . C 2 -57.189 17.288 -7.177 1 48.45 ? CMB HEM 1450 A 1 HETATM 20 C CAB HEM . . . C 2 -59.117 17.778 -4.586 1 54.01 ? CAB HEM 1450 A 1 HETATM 21 C CBB HEM . . . C 2 -59.429 18.73 -5.456 1 57.15 ? CBB HEM 1450 A 1 HETATM 22 C C1C HEM . . . C 2 -58.306 14.586 -1.689 1 42.53 ? C1C HEM 1450 A 1 HETATM 23 C C2C HEM . . . C 2 -58.964 14.555 -0.452 1 42.94 ? C2C HEM 1450 A 1 HETATM 24 C C3C HEM . . . C 2 -58.447 13.474 0.208 1 44.64 ? C3C HEM 1450 A 1 HETATM 25 C C4C HEM . . . C 2 -57.475 12.865 -0.65 1 42.82 ? C4C HEM 1450 A 1 HETATM 26 C CMC HEM . . . C 2 -60.037 15.469 0.105 1 40.03 ? CMC HEM 1450 A 1 HETATM 27 C CAC HEM . . . C 2 -58.912 13.138 1.557 1 48.46 ? CAC HEM 1450 A 1 HETATM 28 C CBC HEM . . . C 2 -58.428 12.137 2.277 1 51.81 ? CBC HEM 1450 A 1 HETATM 29 C C1D HEM . . . C 2 -55.836 11.293 -1.304 1 44 ? C1D HEM 1450 A 1 HETATM 30 C C2D HEM . . . C 2 -55.071 10.098 -0.974 1 48.79 ? C2D HEM 1450 A 1 HETATM 31 C C3D HEM . . . C 2 -54.347 9.771 -2.034 1 50.92 ? C3D HEM 1450 A 1 HETATM 32 C C4D HEM . . . C 2 -54.659 10.8 -3.01 1 50.07 ? C4D HEM 1450 A 1 HETATM 33 C CMD HEM . . . C 2 -55.072 9.334 0.309 1 52.3 ? CMD HEM 1450 A 1 HETATM 34 C CAD HEM . . . C 2 -53.343 8.654 -2.107 1 55.02 ? CAD HEM 1450 A 1 HETATM 35 C CBD HEM . . . C 2 -53.728 7.313 -2.719 1 60.3 ? CBD HEM 1450 A 1 HETATM 36 C CGD HEM . . . C 2 -52.641 6.326 -2.344 1 56.43 ? CGD HEM 1450 A 1 HETATM 37 O O1D HEM . . . C 2 -52.824 5.116 -2.571 1 54.77 ? O1D HEM 1450 A 1 HETATM 38 O O2D HEM . . . C 2 -51.562 6.702 -1.822 1 53.79 ? O2D HEM 1450 A 1 HETATM 39 N NA HEM . . . C 2 -55.115 12.81 -5.004 1 44.98 ? NA HEM 1450 A 1 HETATM 40 N NB HEM . . . C 2 -56.957 14.836 -4.389 1 45.03 ? NB HEM 1450 A 1 HETATM 41 N NC HEM . . . C 2 -57.407 13.582 -1.776 1 41.97 ? NC HEM 1450 A 1 HETATM 42 N ND HEM . . . C 2 -55.583 11.667 -2.534 1 45.22 ? ND HEM 1450 A 1 HETATM 43 FE FE HEM . . . C 2 -56.241 13.16 -3.413 1 43.19 ? FE HEM 1450 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #