data_5V5Z # _model_server_result.job_id r2g_NRUTu0eyQrFMxw9whQ _model_server_result.datetime_utc '2024-11-29 17:11:32' _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 5v5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5V5Z # _exptl.entry_id 5V5Z _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 5V5Z _cell.length_a 91.94 _cell.length_b 92.51 _cell.length_c 101.53 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V5Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 2 21 21' # _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N39 1YN . A 1YN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? # _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 222 n n CHA C4D HEM doub 223 n n CHA HHA HEM sing 224 n n CHB C4A HEM sing 225 n n CHB C1B HEM doub 226 n n CHB HHB HEM sing 227 n n CHC C4B HEM sing 228 n n CHC C1C HEM doub 229 n n CHC HHC HEM sing 230 n n CHD C4C HEM doub 231 n n CHD C1D HEM sing 232 n n CHD HHD HEM sing 233 n n C1A C2A HEM doub 234 n y C1A NA HEM sing 235 n y C2A C3A HEM sing 236 n y C2A CAA HEM sing 237 n n C3A C4A HEM doub 238 n y C3A CMA HEM sing 239 n n C4A NA HEM sing 240 n y CMA HMA HEM sing 241 n n CMA HMAA HEM sing 242 n n CMA HMAB HEM sing 243 n n CAA CBA HEM sing 244 n n CAA HAA HEM sing 245 n n CAA HAAA HEM sing 246 n n CBA CGA HEM sing 247 n n CBA HBA HEM sing 248 n n CBA HBAA HEM sing 249 n n CGA O1A HEM doub 250 n n CGA O2A HEM sing 251 n n C1B C2B HEM sing 252 n n C1B NB HEM sing 253 n n C2B C3B HEM doub 254 n n C2B CMB HEM sing 255 n n C3B C4B HEM sing 256 n n C3B CAB HEM sing 257 n n C4B NB HEM doub 258 n n CMB HMB HEM sing 259 n n CMB HMBA HEM sing 260 n n CMB HMBB HEM sing 261 n n CAB CBB HEM doub 262 n n CAB HAB HEM sing 263 n n CBB HBB HEM sing 264 n n CBB HBBA HEM sing 265 n n C1C C2C HEM sing 266 n y C1C NC HEM sing 267 n y C2C C3C HEM doub 268 n y C2C CMC HEM sing 269 n n C3C C4C HEM sing 270 n y C3C CAC HEM sing 271 n n C4C NC HEM sing 272 n y CMC HMC HEM sing 273 n n CMC HMCA HEM sing 274 n n CMC HMCB HEM sing 275 n n CAC CBC HEM doub 276 n n CAC HAC HEM sing 277 n n CBC HBC HEM sing 278 n n CBC HBCA HEM sing 279 n n C1D C2D HEM sing 280 n n C1D ND HEM doub 281 n n C2D C3D HEM doub 282 n n C2D CMD HEM sing 283 n n C3D C4D HEM sing 284 n n C3D CAD HEM sing 285 n n C4D ND HEM sing 286 n n CMD HMD HEM sing 287 n n CMD HMDA HEM sing 288 n n CMD HMDB HEM sing 289 n n CAD CBD HEM sing 290 n n CAD HAD HEM sing 291 n n CAD HADA HEM sing 292 n n CBD CGD HEM sing 293 n n CBD HBD HEM sing 294 n n CBD HBDA HEM sing 295 n n CGD O1D HEM doub 296 n n CGD O2D HEM sing 297 n n O2A H2A HEM sing 298 n n O2D H2D HEM sing 299 n n FE NA HEM sing 300 n n FE NB HEM sing 301 n n FE NC HEM sing 302 n n FE ND HEM sing 303 n n # _atom_sites.entry_id 5V5Z _atom_sites.fract_transf_matrix[1][1] 0.010877 _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] 0.01081 _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] 0.009849 _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 1YN A 1 602 701 1YN 1YN . # 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 -43.45 -7.962 24.299 1 55.8 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -45.893 -11.121 27.008 1 48.52 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -49.009 -11.778 23.371 1 46.6 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -45.985 -9.472 20.478 1 44.14 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -43.827 -8.72 25.377 1 51.13 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -43.196 -8.738 26.678 1 47.45 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -43.886 -9.596 27.429 1 54.63 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -44.96 -10.176 26.628 1 52.84 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -43.557 -9.914 28.898 1 48.66 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -41.992 -7.901 27.134 1 43.85 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -40.655 -8.548 26.833 1 34.92 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -39.532 -7.734 27.453 1 49.76 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -38.412 -8.314 27.482 1 45.57 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -39.71 -6.532 27.904 1 43.91 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -46.983 -11.542 26.272 1 48.46 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -48.102 -12.349 26.737 1 47.83 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -48.931 -12.537 25.705 1 49.41 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -48.388 -11.833 24.573 1 49.53 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -48.263 -12.916 28.173 1 50.94 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -50.279 -13.275 25.578 1 42.61 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -51.076 -13.503 26.614 1 50.02 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -48.471 -11.249 22.253 1 56.05 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -49.018 -11.351 20.906 1 54.69 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -48.143 -10.713 20.107 1 52.81 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -47.068 -10.176 20.92 1 53.57 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -50.339 -12.083 20.561 1 42.71 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -48.187 -10.449 18.58 1 55.94 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -49.322 -10.348 17.883 1 57.05 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -45.079 -8.843 21.267 1 45.83 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -44.118 -7.887 20.798 1 54.64 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -43.399 -7.454 21.837 1 51.11 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -43.913 -8.128 23.011 1 51.93 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -43.976 -7.46 19.327 1 38.66 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -42.277 -6.399 21.77 1 43.5 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -40.988 -6.792 22.473 1 43.83 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -40.011 -5.669 22.234 1 51.64 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -40.476 -4.547 21.893 1 50.59 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -38.778 -5.872 22.383 1 48.62 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -44.895 -9.596 25.374 1 50.69 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -47.205 -11.255 24.926 1 50.42 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -47.298 -10.542 22.234 1 57.89 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -44.941 -8.975 22.628 1 47.48 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -46.323 -10.093 23.772 1 48.85 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #