data_4XYD # _model_server_result.job_id cAMZMBYCmagWmrzEAd6QVw _model_server_result.datetime_utc '2024-11-21 13:43:11' _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 4xyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4XYD # _exptl.entry_id 4XYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 4XYD _cell.length_a 86.22 _cell.length_b 98.83 _cell.length_c 126.78 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XYD _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 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 ? 3 C N N ? 3 F 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 B SG CYS 62 B CYS 62 1_555 H CAB HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? covale ? covale2 B SG CYS 65 B CYS 65 1_555 H CAC HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? metalc ? metalc1 A NE2 HIS 53 A HIS 53 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc2 A OE1 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 A OE2 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc4 A ND1 HIS 194 A HIS 194 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc5 A OE1 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 A OE2 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc7 A NE2 HIS 245 A HIS 245 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc8 A NE2 HIS 246 A HIS 246 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc9 A NE2 HIS 334 A HIS 334 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc10 A NE2 HIS 336 A HIS 336 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc11 C O1D HEM . A HEM 501 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc12 D O2 UNL . A UNL 502 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc13 D O2 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc14 D O1 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc15 E CA CA . A CA 503 1_555 F O1A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc16 E CA CA . A CA 503 1_555 F O2A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? metalc ? metalc17 E CA CA . A CA 503 1_555 B O GLY 72 B GLY 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc18 E CA CA . A CA 503 1_555 B OH TYR 74 B TYR 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc19 B OE1 GLU 49 B GLU 49 1_555 I CU CU . B CU 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc20 B ND1 HIS 52 B HIS 52 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc21 B NE2 HIS 66 B HIS 66 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc22 B SD MET 116 B MET 116 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc23 B OE1 GLU 124 B GLU 124 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc24 I CU CU . B CU 202 1_555 K O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? # _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 213 n n CHA C4D HEM doub 214 n n CHA HHA HEM sing 215 n n CHB C4A HEM sing 216 n n CHB C1B HEM doub 217 n n CHB HHB HEM sing 218 n n CHC C4B HEM sing 219 n n CHC C1C HEM doub 220 n n CHC HHC HEM sing 221 n n CHD C4C HEM doub 222 n n CHD C1D HEM sing 223 n n CHD HHD HEM sing 224 n n C1A C2A HEM doub 225 n y C1A NA HEM sing 226 n y C2A C3A HEM sing 227 n y C2A CAA HEM sing 228 n n C3A C4A HEM doub 229 n y C3A CMA HEM sing 230 n n C4A NA HEM sing 231 n y CMA HMA HEM sing 232 n n CMA HMAA HEM sing 233 n n CMA HMAB HEM sing 234 n n CAA CBA HEM sing 235 n n CAA HAA HEM sing 236 n n CAA HAAA HEM sing 237 n n CBA CGA HEM sing 238 n n CBA HBA HEM sing 239 n n CBA HBAA HEM sing 240 n n CGA O1A HEM doub 241 n n CGA O2A HEM sing 242 n n C1B C2B HEM sing 243 n n C1B NB HEM sing 244 n n C2B C3B HEM doub 245 n n C2B CMB HEM sing 246 n n C3B C4B HEM sing 247 n n C3B CAB HEM sing 248 n n C4B NB HEM doub 249 n n CMB HMB HEM sing 250 n n CMB HMBA HEM sing 251 n n CMB HMBB HEM sing 252 n n CAB CBB HEM doub 253 n n CAB HAB HEM sing 254 n n CBB HBB HEM sing 255 n n CBB HBBA HEM sing 256 n n C1C C2C HEM sing 257 n y C1C NC HEM sing 258 n y C2C C3C HEM doub 259 n y C2C CMC HEM sing 260 n n C3C C4C HEM sing 261 n y C3C CAC HEM sing 262 n n C4C NC HEM sing 263 n y CMC HMC HEM sing 264 n n CMC HMCA HEM sing 265 n n CMC HMCB HEM sing 266 n n CAC CBC HEM doub 267 n n CAC HAC HEM sing 268 n n CBC HBC HEM sing 269 n n CBC HBCA HEM sing 270 n n C1D C2D HEM sing 271 n n C1D ND HEM doub 272 n n C2D C3D HEM doub 273 n n C2D CMD HEM sing 274 n n C3D C4D HEM sing 275 n n C3D CAD HEM sing 276 n n C4D ND HEM sing 277 n n CMD HMD HEM sing 278 n n CMD HMDA HEM sing 279 n n CMD HMDB HEM sing 280 n n CAD CBD HEM sing 281 n n CAD HAD HEM sing 282 n n CAD HADA HEM sing 283 n n CBD CGD HEM sing 284 n n CBD HBD HEM sing 285 n n CBD HBDA HEM sing 286 n n CGD O1D HEM doub 287 n n CGD O2D HEM sing 288 n n O2A H2A HEM sing 289 n n O2D H2D HEM sing 290 n n FE NA HEM sing 291 n n FE NB HEM sing 292 n n FE NC HEM sing 293 n n FE ND HEM sing 294 n n # _atom_sites.entry_id 4XYD _atom_sites.fract_transf_matrix[1][1] 0.011598 _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] 0.010118 _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] 0.007888 _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 3 HEM A 1 501 500 HEM HEM . D 4 UNL A 1 502 1 UNL UNL . E 5 CA A 1 503 700 CA CA . F 3 HEM A 1 504 600 HEM HEM . G 6 FE A 1 505 601 FE FE . H 7 HEC B 1 201 500 HEC HEC . I 8 CU B 1 202 600 CU CU . J 9 HOH A 1 601 13 HOH HOH . J 9 HOH A 2 602 17 HOH HOH . J 9 HOH A 3 603 11 HOH HOH . J 9 HOH A 4 604 15 HOH HOH . J 9 HOH A 5 605 2 HOH HOH . J 9 HOH A 6 606 12 HOH HOH . J 9 HOH A 7 607 8 HOH HOH . J 9 HOH A 8 608 5 HOH HOH . J 9 HOH A 9 609 4 HOH HOH . J 9 HOH A 10 610 14 HOH HOH . J 9 HOH A 11 611 1 HOH HOH . J 9 HOH A 12 612 3 HOH HOH . K 9 HOH B 1 301 10 HOH HOH . K 9 HOH B 2 302 7 HOH HOH . K 9 HOH B 3 303 9 HOH HOH . K 9 HOH B 4 304 6 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 3 27.358 -13.089 -34.798 1 36.7 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 3 31.068 -13.397 -31.668 1 36.2 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 3 29.958 -18.07 -30.95 1 36.45 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 3 25.76 -17.349 -33.228 1 36.28 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 3 28.465 -12.805 -34.067 1 36.79 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 3 29.16 -11.569 -34.099 1 38.54 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 3 30.195 -11.664 -33.221 1 38.33 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 3 30.152 -12.952 -32.631 1 38.93 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 3 31.21 -10.599 -32.905 1 36.82 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 3 28.842 -10.359 -34.937 1 40.05 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 3 27.849 -9.51 -34.163 1 45.57 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 3 27.759 -8.153 -34.803 1 49.45 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 3 27.301 -8.026 -35.97 1 46.82 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 3 28.138 -7.16 -34.138 1 53.9 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 3 31.1 -14.71 -31.216 1 36.06 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 3 32.106 -15.211 -30.345 1 38.78 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 3 31.802 -16.524 -30.156 1 39.08 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 3 30.573 -16.818 -30.919 1 36.79 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 3 33.297 -14.509 -29.708 1 37.85 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 3 32.556 -17.45 -29.311 1 42.59 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 3 33.109 -18.551 -29.808 1 50.75 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 3 28.671 -18.281 -31.413 1 35.28 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 3 27.875 -19.43 -31.189 1 36.27 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 3 26.682 -19.165 -31.857 1 38.4 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 3 26.765 -17.905 -32.485 1 37.07 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 3 28.201 -20.696 -30.402 1 33.15 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 3 25.501 -20.017 -31.958 1 41.38 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 3 25.604 -21.058 -32.763 1 47.43 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 3 25.915 -16.107 -33.832 1 37.33 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 3 24.854 -15.589 -34.703 1 38.25 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 3 25.281 -14.4 -35.155 1 39.71 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 3 26.614 -14.213 -34.537 1 36.91 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 3 23.547 -16.261 -35.045 1 37.25 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 3 24.498 -13.461 -36.064 1 41.65 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 3 23.923 -12.474 -35.036 1 48.67 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 3 22.814 -11.496 -35.39 1 55.52 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 3 22.731 -10.951 -36.527 1 58.08 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 3 21.978 -11.201 -34.481 1 56.76 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 3 29.107 -13.653 -33.216 1 36.2 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 3 30.254 -15.697 -31.558 1 36.33 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 3 28 -17.405 -32.225 1 35.05 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 3 26.976 -15.272 -33.793 1 36.66 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 3 28.542 -15.473 -32.734 1 35.88 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #