data_4YTP # _model_server_result.job_id Z3oWOn9Pe3Fc6rOUjJeLBA _model_server_result.datetime_utc '2024-11-06 03:10:41' _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 4ytp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 4YTP # _exptl.entry_id 4YTP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 9 _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 4YTP _cell.length_a 71.429 _cell.length_b 84.008 _cell.length_c 294.817 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YTP _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L,M,N _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 9 _struct_asym.id I _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 B SG CYS 93 B CYS 65 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc2 B SG CYS 98 B CYS 70 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc3 B SG CYS 101 B CYS 73 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc4 B SG CYS 113 B CYS 85 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc5 B SG CYS 186 B CYS 158 1_555 G FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc6 B SG CYS 189 B CYS 161 1_555 G FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc7 B SG CYS 192 B CYS 164 1_555 G FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc8 B SG CYS 196 B CYS 168 1_555 H FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc9 B SG CYS 243 B CYS 215 1_555 H FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc10 B SG CYS 249 B CYS 221 1_555 H FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc11 B SG CYS 253 B CYS 225 1_555 G FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc12 C NE2 HIS 127 C HIS 101 1_555 I FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc13 I FE HEM . C HEM 301 1_555 D NE2 HIS 102 D HIS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 278 n n CHA C4D HEM doub 279 n n CHA HHA HEM sing 280 n n CHB C4A HEM sing 281 n n CHB C1B HEM doub 282 n n CHB HHB HEM sing 283 n n CHC C4B HEM sing 284 n n CHC C1C HEM doub 285 n n CHC HHC HEM sing 286 n n CHD C4C HEM doub 287 n n CHD C1D HEM sing 288 n n CHD HHD HEM sing 289 n n C1A C2A HEM doub 290 n y C1A NA HEM sing 291 n y C2A C3A HEM sing 292 n y C2A CAA HEM sing 293 n n C3A C4A HEM doub 294 n y C3A CMA HEM sing 295 n n C4A NA HEM sing 296 n y CMA HMA HEM sing 297 n n CMA HMAA HEM sing 298 n n CMA HMAB HEM sing 299 n n CAA CBA HEM sing 300 n n CAA HAA HEM sing 301 n n CAA HAAA HEM sing 302 n n CBA CGA HEM sing 303 n n CBA HBA HEM sing 304 n n CBA HBAA HEM sing 305 n n CGA O1A HEM doub 306 n n CGA O2A HEM sing 307 n n C1B C2B HEM sing 308 n n C1B NB HEM sing 309 n n C2B C3B HEM doub 310 n n C2B CMB HEM sing 311 n n C3B C4B HEM sing 312 n n C3B CAB HEM sing 313 n n C4B NB HEM doub 314 n n CMB HMB HEM sing 315 n n CMB HMBA HEM sing 316 n n CMB HMBB HEM sing 317 n n CAB CBB HEM doub 318 n n CAB HAB HEM sing 319 n n CBB HBB HEM sing 320 n n CBB HBBA HEM sing 321 n n C1C C2C HEM sing 322 n y C1C NC HEM sing 323 n y C2C C3C HEM doub 324 n y C2C CMC HEM sing 325 n n C3C C4C HEM sing 326 n y C3C CAC HEM sing 327 n n C4C NC HEM sing 328 n y CMC HMC HEM sing 329 n n CMC HMCA HEM sing 330 n n CMC HMCB HEM sing 331 n n CAC CBC HEM doub 332 n n CAC HAC HEM sing 333 n n CBC HBC HEM sing 334 n n CBC HBCA HEM sing 335 n n C1D C2D HEM sing 336 n n C1D ND HEM doub 337 n n C2D C3D HEM doub 338 n n C2D CMD HEM sing 339 n n C3D C4D HEM sing 340 n n C3D CAD HEM sing 341 n n C4D ND HEM sing 342 n n CMD HMD HEM sing 343 n n CMD HMDA HEM sing 344 n n CMD HMDB HEM sing 345 n n CAD CBD HEM sing 346 n n CAD HAD HEM sing 347 n n CAD HADA HEM sing 348 n n CBD CGD HEM sing 349 n n CBD HBD HEM sing 350 n n CBD HBDA HEM sing 351 n n CGD O1D HEM doub 352 n n CGD O2D HEM sing 353 n n O2A H2A HEM sing 354 n n O2D H2D HEM sing 355 n n FE NA HEM sing 356 n n FE NB HEM sing 357 n n FE NC HEM sing 358 n n FE ND HEM sing 359 n n # _atom_sites.entry_id 4YTP _atom_sites.fract_transf_matrix[1][1] 0.014 _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] 0.011904 _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] 0.003392 _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 E 5 FAD A 1 701 702 FAD FAD . F 6 FES B 1 301 302 FES FES . G 7 SF4 B 1 302 303 SF4 SF4 . H 8 F3S B 1 303 304 F3S F3S . I 9 HEM C 1 301 301 HEM HEM . J 10 E23 C 1 302 302 E23 n23 . K 11 HOH A 1 801 9 HOH HOH . K 11 HOH A 2 802 12 HOH HOH . K 11 HOH A 3 803 6 HOH HOH . K 11 HOH A 4 804 19 HOH HOH . K 11 HOH A 5 805 10 HOH HOH . K 11 HOH A 6 806 7 HOH HOH . K 11 HOH A 7 807 15 HOH HOH . K 11 HOH A 8 808 1 HOH HOH . K 11 HOH A 9 809 11 HOH HOH . L 11 HOH B 1 401 18 HOH HOH . L 11 HOH B 2 402 17 HOH HOH . L 11 HOH B 3 403 22 HOH HOH . L 11 HOH B 4 404 14 HOH HOH . L 11 HOH B 5 405 16 HOH HOH . L 11 HOH B 6 406 21 HOH HOH . M 11 HOH C 1 401 13 HOH HOH . M 11 HOH C 2 402 8 HOH HOH . M 11 HOH C 3 403 2 HOH HOH . M 11 HOH C 4 404 4 HOH HOH . M 11 HOH C 5 405 20 HOH HOH . N 11 HOH D 1 201 5 HOH HOH . N 11 HOH D 2 202 3 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 . . . I 9 -33.68 -27.369 65.166 1 55.99 ? CHA HEM 301 C 1 HETATM 2 C CHB HEM . . . I 9 -37.57 -24.614 65.856 1 64.59 ? CHB HEM 301 C 1 HETATM 3 C CHC HEM . . . I 9 -37.617 -25.888 70.54 1 60.73 ? CHC HEM 301 C 1 HETATM 4 C CHD HEM . . . I 9 -33.973 -28.902 69.713 1 57.77 ? CHD HEM 301 C 1 HETATM 5 C C1A HEM . . . I 9 -34.726 -26.534 64.959 1 57 ? C1A HEM 301 C 1 HETATM 6 C C2A HEM . . . I 9 -35.093 -26.018 63.701 1 59.64 ? C2A HEM 301 C 1 HETATM 7 C C3A HEM . . . I 9 -36.198 -25.248 63.901 1 59.98 ? C3A HEM 301 C 1 HETATM 8 C C4A HEM . . . I 9 -36.499 -25.283 65.276 1 61.16 ? C4A HEM 301 C 1 HETATM 9 C CMA HEM . . . I 9 -36.981 -24.483 62.86 1 60.3 ? CMA HEM 301 C 1 HETATM 10 C CAA HEM . . . I 9 -34.416 -26.304 62.372 1 61.57 ? CAA HEM 301 C 1 HETATM 11 C CBA HEM . . . I 9 -33.371 -25.258 61.979 1 63.2 ? CBA HEM 301 C 1 HETATM 12 C CGA HEM . . . I 9 -33.166 -25.293 60.485 1 63.26 ? CGA HEM 301 C 1 HETATM 13 O O1A HEM . . . I 9 -32.133 -25.821 60.019 1 63.57 ? O1A HEM 301 C 1 HETATM 14 O O2A HEM . . . I 9 -34.024 -24.797 59.712 1 64.84 ? O2A HEM 301 C 1 HETATM 15 C C1B HEM . . . I 9 -37.931 -24.708 67.212 1 62.45 ? C1B HEM 301 C 1 HETATM 16 C C2B HEM . . . I 9 -39.033 -24.012 67.812 1 62.45 ? C2B HEM 301 C 1 HETATM 17 C C3B HEM . . . I 9 -39.041 -24.374 69.139 1 61.91 ? C3B HEM 301 C 1 HETATM 18 C C4B HEM . . . I 9 -37.908 -25.3 69.312 1 60.24 ? C4B HEM 301 C 1 HETATM 19 C CMB HEM . . . I 9 -39.992 -23.067 67.113 1 61.13 ? CMB HEM 301 C 1 HETATM 20 C CAB HEM . . . I 9 -39.942 -23.997 70.246 1 61.27 ? CAB HEM 301 C 1 HETATM 21 C CBB HEM . . . I 9 -41.003 -23.236 70.09 1 61.82 ? CBB HEM 301 C 1 HETATM 22 C C1C HEM . . . I 9 -36.651 -26.865 70.739 1 63.38 ? C1C HEM 301 C 1 HETATM 23 C C2C HEM . . . I 9 -36.495 -27.645 71.909 1 64.06 ? C2C HEM 301 C 1 HETATM 24 C C3C HEM . . . I 9 -35.435 -28.517 71.668 1 63.64 ? C3C HEM 301 C 1 HETATM 25 C C4C HEM . . . I 9 -34.984 -28.256 70.339 1 61.67 ? C4C HEM 301 C 1 HETATM 26 C CMC HEM . . . I 9 -37.318 -27.521 73.173 1 63.69 ? CMC HEM 301 C 1 HETATM 27 C CAC HEM . . . I 9 -34.854 -29.566 72.533 1 63.85 ? CAC HEM 301 C 1 HETATM 28 C CBC HEM . . . I 9 -35.353 -29.927 73.709 1 66.13 ? CBC HEM 301 C 1 HETATM 29 C C1D HEM . . . I 9 -33.652 -28.665 68.395 1 55.34 ? C1D HEM 301 C 1 HETATM 30 C C2D HEM . . . I 9 -32.54 -29.397 67.811 1 54.25 ? C2D HEM 301 C 1 HETATM 31 C C3D HEM . . . I 9 -32.467 -28.973 66.551 1 53.22 ? C3D HEM 301 C 1 HETATM 32 C C4D HEM . . . I 9 -33.516 -27.983 66.38 1 55.37 ? C4D HEM 301 C 1 HETATM 33 C CMD HEM . . . I 9 -31.656 -30.431 68.47 1 55.03 ? CMD HEM 301 C 1 HETATM 34 C CAD HEM . . . I 9 -31.476 -29.39 65.504 1 53.25 ? CAD HEM 301 C 1 HETATM 35 C CBD HEM . . . I 9 -30.427 -28.273 65.415 1 53.63 ? CBD HEM 301 C 1 HETATM 36 C CGD HEM . . . I 9 -29.969 -28.052 63.997 1 56.3 ? CGD HEM 301 C 1 HETATM 37 O O1D HEM . . . I 9 -30.197 -28.913 63.11 1 56.16 ? O1D HEM 301 C 1 HETATM 38 O O2D HEM . . . I 9 -29.34 -27.003 63.711 1 55.41 ? O2D HEM 301 C 1 HETATM 39 N NA HEM . . . I 9 -35.593 -26.089 65.913 1 58.1 ? NA HEM 301 C 1 HETATM 40 N NB HEM . . . I 9 -37.306 -25.421 68.133 1 59.31 ? NB HEM 301 C 1 HETATM 41 N NC HEM . . . I 9 -35.735 -27.265 69.806 1 62.48 ? NC HEM 301 C 1 HETATM 42 N ND HEM . . . I 9 -34.205 -27.817 67.51 1 57.81 ? ND HEM 301 C 1 HETATM 43 FE FE HEM . . . I 9 -35.676 -26.663 67.818 1 60.81 ? FE HEM 301 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #