data_5YSW # _model_server_result.job_id KSgydg2hC4y6iUW_wje6qg _model_server_result.datetime_utc '2024-11-05 01:16:31' _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 5ysw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5YSW # _exptl.entry_id 5YSW _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 94 _cell.angle_gamma 90 _cell.entry_id 5YSW _cell.length_a 35.082 _cell.length_b 70.709 _cell.length_c 80.975 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YSW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D _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 # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 387 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 366 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 2.435 _struct_conn.pdbx_value_order ? # _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 235 n n CHA C4D HEM doub 236 n n CHA HHA HEM sing 237 n n CHB C4A HEM sing 238 n n CHB C1B HEM doub 239 n n CHB HHB HEM sing 240 n n CHC C4B HEM sing 241 n n CHC C1C HEM doub 242 n n CHC HHC HEM sing 243 n n CHD C4C HEM doub 244 n n CHD C1D HEM sing 245 n n CHD HHD HEM sing 246 n n C1A C2A HEM doub 247 n y C1A NA HEM sing 248 n y C2A C3A HEM sing 249 n y C2A CAA HEM sing 250 n n C3A C4A HEM doub 251 n y C3A CMA HEM sing 252 n n C4A NA HEM sing 253 n y CMA HMA HEM sing 254 n n CMA HMAA HEM sing 255 n n CMA HMAB HEM sing 256 n n CAA CBA HEM sing 257 n n CAA HAA HEM sing 258 n n CAA HAAA HEM sing 259 n n CBA CGA HEM sing 260 n n CBA HBA HEM sing 261 n n CBA HBAA HEM sing 262 n n CGA O1A HEM doub 263 n n CGA O2A HEM sing 264 n n C1B C2B HEM sing 265 n n C1B NB HEM sing 266 n n C2B C3B HEM doub 267 n n C2B CMB HEM sing 268 n n C3B C4B HEM sing 269 n n C3B CAB HEM sing 270 n n C4B NB HEM doub 271 n n CMB HMB HEM sing 272 n n CMB HMBA HEM sing 273 n n CMB HMBB HEM sing 274 n n CAB CBB HEM doub 275 n n CAB HAB HEM sing 276 n n CBB HBB HEM sing 277 n n CBB HBBA HEM sing 278 n n C1C C2C HEM sing 279 n y C1C NC HEM sing 280 n y C2C C3C HEM doub 281 n y C2C CMC HEM sing 282 n n C3C C4C HEM sing 283 n y C3C CAC HEM sing 284 n n C4C NC HEM sing 285 n y CMC HMC HEM sing 286 n n CMC HMCA HEM sing 287 n n CMC HMCB HEM sing 288 n n CAC CBC HEM doub 289 n n CAC HAC HEM sing 290 n n CBC HBC HEM sing 291 n n CBC HBCA HEM sing 292 n n C1D C2D HEM sing 293 n n C1D ND HEM doub 294 n n C2D C3D HEM doub 295 n n C2D CMD HEM sing 296 n n C3D C4D HEM sing 297 n n C3D CAD HEM sing 298 n n C4D ND HEM sing 299 n n CMD HMD HEM sing 300 n n CMD HMDA HEM sing 301 n n CMD HMDB HEM sing 302 n n CAD CBD HEM sing 303 n n CAD HAD HEM sing 304 n n CAD HADA HEM sing 305 n n CBD CGD HEM sing 306 n n CBD HBD HEM sing 307 n n CBD HBDA HEM sing 308 n n CGD O1D HEM doub 309 n n CGD O2D HEM sing 310 n n O2A H2A HEM sing 311 n n O2D H2D HEM sing 312 n n FE NA HEM sing 313 n n FE NB HEM sing 314 n n FE NC HEM sing 315 n n FE ND HEM sing 316 n n # _atom_sites.entry_id 5YSW _atom_sites.fract_transf_matrix[1][1] 0.028505 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001994 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014142 _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] 0.01238 _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 1 501 501 HEM HEM . C 3 9LF A 1 502 1 9LF L3 . D 4 HOH A 1 601 55 HOH HOH . D 4 HOH A 2 602 40 HOH HOH . D 4 HOH A 3 603 39 HOH HOH . D 4 HOH A 4 604 26 HOH HOH . D 4 HOH A 5 605 22 HOH HOH . D 4 HOH A 6 606 16 HOH HOH . D 4 HOH A 7 607 30 HOH HOH . D 4 HOH A 8 608 20 HOH HOH . D 4 HOH A 9 609 13 HOH HOH . D 4 HOH A 10 610 61 HOH HOH . D 4 HOH A 11 611 29 HOH HOH . D 4 HOH A 12 612 60 HOH HOH . D 4 HOH A 13 613 37 HOH HOH . D 4 HOH A 14 614 57 HOH HOH . D 4 HOH A 15 615 5 HOH HOH . D 4 HOH A 16 616 8 HOH HOH . D 4 HOH A 17 617 6 HOH HOH . D 4 HOH A 18 618 45 HOH HOH . D 4 HOH A 19 619 38 HOH HOH . D 4 HOH A 20 620 47 HOH HOH . D 4 HOH A 21 621 51 HOH HOH . D 4 HOH A 22 622 58 HOH HOH . D 4 HOH A 23 623 28 HOH HOH . D 4 HOH A 24 624 62 HOH HOH . D 4 HOH A 25 625 12 HOH HOH . D 4 HOH A 26 626 15 HOH HOH . D 4 HOH A 27 627 42 HOH HOH . D 4 HOH A 28 628 1 HOH HOH . D 4 HOH A 29 629 33 HOH HOH . D 4 HOH A 30 630 52 HOH HOH . D 4 HOH A 31 631 32 HOH HOH . D 4 HOH A 32 632 35 HOH HOH . D 4 HOH A 33 633 19 HOH HOH . D 4 HOH A 34 634 36 HOH HOH . D 4 HOH A 35 635 21 HOH HOH . D 4 HOH A 36 636 54 HOH HOH . D 4 HOH A 37 637 17 HOH HOH . D 4 HOH A 38 638 18 HOH HOH . D 4 HOH A 39 639 56 HOH HOH . D 4 HOH A 40 640 48 HOH HOH . D 4 HOH A 41 641 10 HOH HOH . D 4 HOH A 42 642 43 HOH HOH . D 4 HOH A 43 643 46 HOH HOH . D 4 HOH A 44 644 41 HOH HOH . D 4 HOH A 45 645 67 HOH HOH . D 4 HOH A 46 646 44 HOH HOH . D 4 HOH A 47 647 34 HOH HOH . D 4 HOH A 48 648 7 HOH HOH . D 4 HOH A 49 649 65 HOH HOH . D 4 HOH A 50 650 2 HOH HOH . D 4 HOH A 51 651 4 HOH HOH . D 4 HOH A 52 652 25 HOH HOH . D 4 HOH A 53 653 9 HOH HOH . D 4 HOH A 54 654 27 HOH HOH . D 4 HOH A 55 655 14 HOH HOH . D 4 HOH A 56 656 50 HOH HOH . D 4 HOH A 57 657 63 HOH HOH . D 4 HOH A 58 658 11 HOH HOH . D 4 HOH A 59 659 31 HOH HOH . D 4 HOH A 60 660 53 HOH HOH . D 4 HOH A 61 661 66 HOH HOH . D 4 HOH A 62 662 49 HOH HOH . D 4 HOH A 63 663 24 HOH HOH . D 4 HOH A 64 664 64 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 . . . B 2 88.707 66.978 264.93 1 22.2 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 89.535 63.395 261.852 1 21.43 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 90.566 66.545 258.413 1 20.56 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 90.316 70.084 261.622 1 22.63 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 88.784 65.736 264.356 1 21.62 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 88.47 64.541 265.02 1 19.94 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 88.693 63.564 264.156 1 19.83 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 89.199 64.119 262.981 1 20.47 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 88.451 62.106 264.434 1 20.67 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 87.911 64.39 266.41 1 19.28 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 89.002 64.286 267.468 1 20.01 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 88.401 64.38 268.871 1 21.23 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 89.158 64.597 269.885 1 20.24 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 87.145 64.212 268.976 1 19.87 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 89.879 63.951 260.624 1 21.98 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 90.131 63.176 259.449 1 22.04 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 90.405 64.073 258.485 1 21.52 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 90.333 65.394 259.099 1 20.64 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 90.106 61.674 259.296 1 22 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 90.672 63.83 257.081 1 22.23 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 90.398 62.668 256.502 1 22.92 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 90.576 67.805 258.976 1 20.56 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 90.768 68.955 258.262 1 19.95 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 90.706 69.968 259.158 1 21.22 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 90.489 69.428 260.457 1 20.85 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 91.019 69.129 256.782 1 19.26 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 90.933 71.319 258.666 1 21.73 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 91.132 72.337 259.466 1 23.75 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 89.841 69.469 262.758 1 24.12 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 89.601 70.248 264.006 1 24.03 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 89.15 69.386 264.913 1 23.58 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 89.129 68.091 264.239 1 23.15 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 89.752 71.731 264.283 1 23.46 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 88.737 69.729 266.333 1 24.93 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 87.198 69.896 266.472 1 26.57 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 86.788 70.231 267.895 1 28.08 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 85.827 71.004 268.125 1 30.12 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 87.392 69.726 268.87 1 29.88 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 89.223 65.453 263.1 1 21.27 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 89.997 65.242 260.349 1 20.81 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 90.359 68.125 260.276 1 20.68 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 89.509 68.195 262.94 1 23.73 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 89.768 66.794 261.725 1 22.88 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #