data_5VV9 # _model_server_result.job_id yPX9TcodsRWYx_Sa-NURQQ _model_server_result.datetime_utc '2024-11-04 20:35:55' _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 5vv9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5VV9 # _exptl.entry_id 5VV9 _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 90 _cell.entry_id 5VV9 _cell.length_a 57.245 _cell.length_b 106.127 _cell.length_c 155.832 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VV9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J,K _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 # 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 G 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 covale ? covale1 A C VAL 344 A VAL 383 1_555 A N CAS 345 A CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 B SG CYS 57 B CYS 96 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc5 B SG CYS 62 B CYS 101 1_555 K ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 G FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? # _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 242 n n CHA C4D HEM doub 243 n n CHA HHA HEM sing 244 n n CHB C4A HEM sing 245 n n CHB C1B HEM doub 246 n n CHB HHB HEM sing 247 n n CHC C4B HEM sing 248 n n CHC C1C HEM doub 249 n n CHC HHC HEM sing 250 n n CHD C4C HEM doub 251 n n CHD C1D HEM sing 252 n n CHD HHD HEM sing 253 n n C1A C2A HEM doub 254 n y C1A NA HEM sing 255 n y C2A C3A HEM sing 256 n y C2A CAA HEM sing 257 n n C3A C4A HEM doub 258 n y C3A CMA HEM sing 259 n n C4A NA HEM sing 260 n y CMA HMA HEM sing 261 n n CMA HMAA HEM sing 262 n n CMA HMAB HEM sing 263 n n CAA CBA HEM sing 264 n n CAA HAA HEM sing 265 n n CAA HAAA HEM sing 266 n n CBA CGA HEM sing 267 n n CBA HBA HEM sing 268 n n CBA HBAA HEM sing 269 n n CGA O1A HEM doub 270 n n CGA O2A HEM sing 271 n n C1B C2B HEM sing 272 n n C1B NB HEM sing 273 n n C2B C3B HEM doub 274 n n C2B CMB HEM sing 275 n n C3B C4B HEM sing 276 n n C3B CAB HEM sing 277 n n C4B NB HEM doub 278 n n CMB HMB HEM sing 279 n n CMB HMBA HEM sing 280 n n CMB HMBB HEM sing 281 n n CAB CBB HEM doub 282 n n CAB HAB HEM sing 283 n n CBB HBB HEM sing 284 n n CBB HBBA HEM sing 285 n n C1C C2C HEM sing 286 n y C1C NC HEM sing 287 n y C2C C3C HEM doub 288 n y C2C CMC HEM sing 289 n n C3C C4C HEM sing 290 n y C3C CAC HEM sing 291 n n C4C NC HEM sing 292 n y CMC HMC HEM sing 293 n n CMC HMCA HEM sing 294 n n CMC HMCB HEM sing 295 n n CAC CBC HEM doub 296 n n CAC HAC HEM sing 297 n n CBC HBC HEM sing 298 n n CBC HBCA HEM sing 299 n n C1D C2D HEM sing 300 n n C1D ND HEM doub 301 n n C2D C3D HEM doub 302 n n C2D CMD HEM sing 303 n n C3D C4D HEM sing 304 n n C3D CAD HEM sing 305 n n C4D ND HEM sing 306 n n CMD HMD HEM sing 307 n n CMD HMDA HEM sing 308 n n CMD HMDB HEM sing 309 n n CAD CBD HEM sing 310 n n CAD HAD HEM sing 311 n n CAD HADA HEM sing 312 n n CBD CGD HEM sing 313 n n CBD HBD HEM sing 314 n n CBD HBDA HEM sing 315 n n CGD O1D HEM doub 316 n n CGD O2D HEM sing 317 n n O2A H2A HEM sing 318 n n O2D H2D HEM sing 319 n n FE NA HEM sing 320 n n FE NB HEM sing 321 n n FE NC HEM sing 322 n n FE ND HEM sing 323 n n # _atom_sites.entry_id 5VV9 _atom_sites.fract_transf_matrix[1][1] 0.017469 _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] 0.009423 _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] 0.006417 _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 1 501 500 HEM HEM . D 3 H4B A 1 502 600 H4B BH4 . E 4 9OG A 1 503 800 9OG 2P7 . F 5 GOL A 1 504 880 GOL GOL . G 2 HEM B 1 501 500 HEM HEM . H 3 H4B B 1 502 600 H4B BH4 . I 4 9OG B 1 503 800 9OG 2P7 . J 5 GOL B 1 504 880 GOL GOL . K 6 ZN B 1 505 900 ZN ZN . # 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 9.1 9.325 35.059 1 42.05 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 4.531 9.273 33.54 1 50.51 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 5.995 7.69 29.231 1 44.94 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 10.425 6.893 31.02 1 50.49 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 7.756 9.561 34.947 1 51.97 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 6.961 10.351 35.868 1 53.77 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 5.689 10.334 35.438 1 51.63 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 5.657 9.532 34.247 1 56.37 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 4.431 11.012 36.036 1 44.43 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 7.538 11.098 37.087 1 53.55 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 7.878 12.499 36.573 1 67 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 8.481 13.451 37.583 1 71.7 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 7.824 13.814 38.598 1 70.46 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 9.634 13.884 37.336 1 70.12 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 4.541 8.857 32.258 1 45.89 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 3.372 8.796 31.438 1 49.01 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 3.735 8.347 30.235 1 49.22 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 5.183 8.131 30.253 1 51.95 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 1.964 9.18 31.931 1 45.23 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 2.748 8.144 29.079 1 54.7 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 3.127 7.48 27.985 1 70.37 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 7.329 7.348 29.325 1 54.87 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 8.183 6.845 28.249 1 54.53 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 9.407 6.626 28.758 1 56.84 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 9.364 6.985 30.156 1 50.7 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 7.731 6.62 26.786 1 47.42 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 10.693 6.098 28.065 1 59.77 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 10.809 5.829 26.762 1 49.94 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 10.504 7.489 32.262 1 43.05 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 11.7 7.579 33.081 1 38 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 11.271 8.346 34.325 1 36.52 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 9.865 8.629 34.163 1 40.64 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 13.121 7.049 32.811 1 36.34 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 12.178 8.699 35.499 1 53.05 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 12.445 10.194 35.431 1 73.62 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 13.775 10.435 36.088 1 85.94 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 14.515 9.439 36.347 1 96.6 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 14.087 11.622 36.352 1 76.53 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 6.922 9.075 33.966 1 51.35 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 5.629 8.456 31.525 1 49.63 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 8.087 7.405 30.475 1 49.09 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 9.444 8.091 32.944 1 35.2 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 7.391 7.98 32.364 1 56.26 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #