data_4YT0 # _model_server_result.job_id jRx0_EutvN9qvZ4TQ7Sdjw _model_server_result.datetime_utc '2024-10-12 10:21:41' _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 4yt0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":201}' # _entry.id 4YT0 # _exptl.entry_id 4YT0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 10 _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 4YT0 _cell.length_a 122.803 _cell.length_b 123.392 _cell.length_c 219.001 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YT0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,I,J,K,L,M,N,O 1 1 E,F,G,H,P,Q,R,S,T,U,V 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 ? 10 N N N ? 10 U 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 disulf ? disulf1 A SG CYS 191 A CYS 191 1_555 A SG CYS 193 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 F SG CYS 89 F CYS 89 1_555 F SG CYS 94 F CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc5 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc6 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc8 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc9 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc11 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc12 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc13 F SG CYS 94 F CYS 94 1_555 R FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc14 F SG CYS 97 F CYS 97 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc15 F SG CYS 109 F CYS 109 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc16 F SG CYS 182 F CYS 182 1_555 S FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc17 F SG CYS 188 F CYS 188 1_555 S FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc18 F SG CYS 192 F CYS 192 1_555 T FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc19 F SG CYS 239 F CYS 239 1_555 T FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc20 F SG CYS 245 F CYS 245 1_555 T FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc21 F SG CYS 249 F CYS 249 1_555 S FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc22 G NE2 HIS 131 G HIS 131 1_555 U FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc23 U FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? # _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 233 n n CHA C4D HEM doub 234 n n CHA HHA HEM sing 235 n n CHB C4A HEM sing 236 n n CHB C1B HEM doub 237 n n CHB HHB HEM sing 238 n n CHC C4B HEM sing 239 n n CHC C1C HEM doub 240 n n CHC HHC HEM sing 241 n n CHD C4C HEM doub 242 n n CHD C1D HEM sing 243 n n CHD HHD HEM sing 244 n n C1A C2A HEM doub 245 n y C1A NA HEM sing 246 n y C2A C3A HEM sing 247 n y C2A CAA HEM sing 248 n n C3A C4A HEM doub 249 n y C3A CMA HEM sing 250 n n C4A NA HEM sing 251 n y CMA HMA HEM sing 252 n n CMA HMAA HEM sing 253 n n CMA HMAB HEM sing 254 n n CAA CBA HEM sing 255 n n CAA HAA HEM sing 256 n n CAA HAAA HEM sing 257 n n CBA CGA HEM sing 258 n n CBA HBA HEM sing 259 n n CBA HBAA HEM sing 260 n n CGA O1A HEM doub 261 n n CGA O2A HEM sing 262 n n C1B C2B HEM sing 263 n n C1B NB HEM sing 264 n n C2B C3B HEM doub 265 n n C2B CMB HEM sing 266 n n C3B C4B HEM sing 267 n n C3B CAB HEM sing 268 n n C4B NB HEM doub 269 n n CMB HMB HEM sing 270 n n CMB HMBA HEM sing 271 n n CMB HMBB HEM sing 272 n n CAB CBB HEM doub 273 n n CAB HAB HEM sing 274 n n CBB HBB HEM sing 275 n n CBB HBBA HEM sing 276 n n C1C C2C HEM sing 277 n y C1C NC HEM sing 278 n y C2C C3C HEM doub 279 n y C2C CMC HEM sing 280 n n C3C C4C HEM sing 281 n y C3C CAC HEM sing 282 n n C4C NC HEM sing 283 n y CMC HMC HEM sing 284 n n CMC HMCA HEM sing 285 n n CMC HMCB HEM sing 286 n n CAC CBC HEM doub 287 n n CAC HAC HEM sing 288 n n CBC HBC HEM sing 289 n n CBC HBCA HEM sing 290 n n C1D C2D HEM sing 291 n n C1D ND HEM doub 292 n n C2D C3D HEM doub 293 n n C2D CMD HEM sing 294 n n C3D C4D HEM sing 295 n n C3D CAD HEM sing 296 n n C4D ND HEM sing 297 n n CMD HMD HEM sing 298 n n CMD HMDA HEM sing 299 n n CMD HMDB HEM sing 300 n n CAD CBD HEM sing 301 n n CAD HAD HEM sing 302 n n CAD HADA HEM sing 303 n n CBD CGD HEM sing 304 n n CBD HBD HEM sing 305 n n CBD HBDA HEM sing 306 n n CGD O1D HEM doub 307 n n CGD O2D HEM sing 308 n n O2A H2A HEM sing 309 n n O2D H2D HEM sing 310 n n FE NA HEM sing 311 n n FE NB HEM sing 312 n n FE NC HEM sing 313 n n FE ND HEM sing 314 n n # _atom_sites.entry_id 4YT0 _atom_sites.fract_transf_matrix[1][1] 0.008143 _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] 0.008104 _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] 0.004566 _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 I 5 MLI A 1 701 701 MLI MLI . J 6 FAD A 1 702 702 FAD FAD . K 7 FES B 1 301 301 FES FES . L 8 SF4 B 1 302 302 SF4 SF4 . M 9 F3S B 1 303 303 F3S F3S . N 10 HEM C 1 201 201 HEM HEM . O 11 MRN C 1 202 301 MRN DRG . P 5 MLI E 1 701 701 MLI MLI . Q 6 FAD E 1 702 702 FAD FAD . R 7 FES F 1 301 301 FES FES . S 8 SF4 F 1 302 302 SF4 SF4 . T 9 F3S F 1 303 303 F3S F3S . U 10 HEM G 1 201 201 HEM HEM . V 11 MRN G 1 202 301 MRN DRG . # 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 . . . U 10 -40.658 36.149 25.89 1 76.24 ? CHA HEM 201 G 1 HETATM 2 C CHB HEM . . . U 10 -36.016 37.443 25.569 1 75.1 ? CHB HEM 201 G 1 HETATM 3 C CHC HEM . . . U 10 -37.304 42.045 26.411 1 75.94 ? CHC HEM 201 G 1 HETATM 4 C CHD HEM . . . U 10 -41.961 40.794 26.033 1 77.97 ? CHD HEM 201 G 1 HETATM 5 C C1A HEM . . . U 10 -39.3 36.111 25.748 1 74.94 ? C1A HEM 201 G 1 HETATM 6 C C2A HEM . . . U 10 -38.54 34.931 25.54 1 75.38 ? C2A HEM 201 G 1 HETATM 7 C C3A HEM . . . U 10 -37.239 35.303 25.445 1 74.82 ? C3A HEM 201 G 1 HETATM 8 C C4A HEM . . . U 10 -37.186 36.705 25.586 1 74.32 ? C4A HEM 201 G 1 HETATM 9 C CMA HEM . . . U 10 -36.067 34.38 25.218 1 75.38 ? CMA HEM 201 G 1 HETATM 10 C CAA HEM . . . U 10 -39.051 33.509 25.422 1 75.47 ? CAA HEM 201 G 1 HETATM 11 C CBA HEM . . . U 10 -38.855 32.731 26.733 1 75.5 ? CBA HEM 201 G 1 HETATM 12 C CGA HEM . . . U 10 -40.041 31.846 27.034 1 74.85 ? CGA HEM 201 G 1 HETATM 13 O O1A HEM . . . U 10 -40.66 31.267 26.105 1 72.78 ? O1A HEM 201 G 1 HETATM 14 O O2A HEM . . . U 10 -40.404 31.691 28.226 1 74.02 ? O2A HEM 201 G 1 HETATM 15 C C1B HEM . . . U 10 -35.961 38.827 25.793 1 75.09 ? C1B HEM 201 G 1 HETATM 16 C C2B HEM . . . U 10 -34.733 39.547 25.841 1 75.21 ? C2B HEM 201 G 1 HETATM 17 C C3B HEM . . . U 10 -35.031 40.852 26.089 1 74.8 ? C3B HEM 201 G 1 HETATM 18 C C4B HEM . . . U 10 -36.529 40.902 26.195 1 74.49 ? C4B HEM 201 G 1 HETATM 19 C CMB HEM . . . U 10 -33.346 38.975 25.658 1 75.49 ? CMB HEM 201 G 1 HETATM 20 C CAB HEM . . . U 10 -33.978 41.894 26.179 1 75.25 ? CAB HEM 201 G 1 HETATM 21 C CBB HEM . . . U 10 -34.19 43.2 26.308 1 76.97 ? CBB HEM 201 G 1 HETATM 22 C C1C HEM . . . U 10 -38.699 42.117 26.344 1 75.3 ? C1C HEM 201 G 1 HETATM 23 C C2C HEM . . . U 10 -39.45 43.3 26.438 1 76.54 ? C2C HEM 201 G 1 HETATM 24 C C3C HEM . . . U 10 -40.79 42.976 26.332 1 76.73 ? C3C HEM 201 G 1 HETATM 25 C C4C HEM . . . U 10 -40.842 41.557 26.153 1 76.43 ? C4C HEM 201 G 1 HETATM 26 C CMC HEM . . . U 10 -38.923 44.704 26.621 1 77.07 ? CMC HEM 201 G 1 HETATM 27 C CAC HEM . . . U 10 -41.851 44.019 26.377 1 77.37 ? CAC HEM 201 G 1 HETATM 28 C CBC HEM . . . U 10 -43.162 43.831 26.247 1 76.76 ? CBC HEM 201 G 1 HETATM 29 C C1D HEM . . . U 10 -41.919 39.411 25.981 1 76.87 ? C1D HEM 201 G 1 HETATM 30 C C2D HEM . . . U 10 -43.182 38.658 25.946 1 74.89 ? C2D HEM 201 G 1 HETATM 31 C C3D HEM . . . U 10 -42.854 37.364 25.909 1 77.38 ? C3D HEM 201 G 1 HETATM 32 C C4D HEM . . . U 10 -41.365 37.337 25.94 1 76.44 ? C4D HEM 201 G 1 HETATM 33 C CMD HEM . . . U 10 -44.607 39.167 25.94 1 71.66 ? CMD HEM 201 G 1 HETATM 34 C CAD HEM . . . U 10 -43.96 36.309 25.889 1 78.89 ? CAD HEM 201 G 1 HETATM 35 C CBD HEM . . . U 10 -43.632 34.804 25.903 1 77.97 ? CBD HEM 201 G 1 HETATM 36 C CGD HEM . . . U 10 -43.496 34.222 27.301 1 76.13 ? CGD HEM 201 G 1 HETATM 37 O O1D HEM . . . U 10 -43.577 32.981 27.431 1 75.28 ? O1D HEM 201 G 1 HETATM 38 O O2D HEM . . . U 10 -43.321 34.924 28.331 1 72.5 ? O2D HEM 201 G 1 HETATM 39 N NA HEM . . . U 10 -38.457 37.185 25.791 1 73.48 ? NA HEM 201 G 1 HETATM 40 N NB HEM . . . U 10 -36.983 39.66 26.002 1 73.07 ? NB HEM 201 G 1 HETATM 41 N NC HEM . . . U 10 -39.566 41.076 26.203 1 73.59 ? NC HEM 201 G 1 HETATM 42 N ND HEM . . . U 10 -40.843 38.593 25.967 1 75.75 ? ND HEM 201 G 1 HETATM 43 FE FE HEM . . . U 10 -39 39.083 26.035 1 69.16 ? FE HEM 201 G 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #