data_5JKV # _model_server_result.job_id h05ReXab7_sqO-OskjUsvQ _model_server_result.datetime_utc '2024-10-28 13:16:28' _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 5jkv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5JKV # _exptl.entry_id 5JKV _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 90 _cell.angle_gamma 120 _cell.entry_id 5JKV _cell.length_a 140.218 _cell.length_b 140.218 _cell.length_c 119.271 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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,E,F,G,H,I _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 437 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 437 _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 601 _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 2.225 _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 216 n n CHA C4D HEM doub 217 n n CHA HHA HEM sing 218 n n CHB C4A HEM sing 219 n n CHB C1B HEM doub 220 n n CHB HHB HEM sing 221 n n CHC C4B HEM sing 222 n n CHC C1C HEM doub 223 n n CHC HHC HEM sing 224 n n CHD C4C HEM doub 225 n n CHD C1D HEM sing 226 n n CHD HHD HEM sing 227 n n C1A C2A HEM doub 228 n y C1A NA HEM sing 229 n y C2A C3A HEM sing 230 n y C2A CAA HEM sing 231 n n C3A C4A HEM doub 232 n y C3A CMA HEM sing 233 n n C4A NA HEM sing 234 n y CMA HMA HEM sing 235 n n CMA HMAA HEM sing 236 n n CMA HMAB HEM sing 237 n n CAA CBA HEM sing 238 n n CAA HAA HEM sing 239 n n CAA HAAA HEM sing 240 n n CBA CGA HEM sing 241 n n CBA HBA HEM sing 242 n n CBA HBAA HEM sing 243 n n CGA O1A HEM doub 244 n n CGA O2A HEM sing 245 n n C1B C2B HEM sing 246 n n C1B NB HEM sing 247 n n C2B C3B HEM doub 248 n n C2B CMB HEM sing 249 n n C3B C4B HEM sing 250 n n C3B CAB HEM sing 251 n n C4B NB HEM doub 252 n n CMB HMB HEM sing 253 n n CMB HMBA HEM sing 254 n n CMB HMBB HEM sing 255 n n CAB CBB HEM doub 256 n n CAB HAB HEM sing 257 n n CBB HBB HEM sing 258 n n CBB HBBA HEM sing 259 n n C1C C2C HEM sing 260 n y C1C NC HEM sing 261 n y C2C C3C HEM doub 262 n y C2C CMC HEM sing 263 n n C3C C4C HEM sing 264 n y C3C CAC HEM sing 265 n n C4C NC HEM sing 266 n y CMC HMC HEM sing 267 n n CMC HMCA HEM sing 268 n n CMC HMCB HEM sing 269 n n CAC CBC HEM doub 270 n n CAC HAC HEM sing 271 n n CBC HBC HEM sing 272 n n CBC HBCA HEM sing 273 n n C1D C2D HEM sing 274 n n C1D ND HEM doub 275 n n C2D C3D HEM doub 276 n n C2D CMD HEM sing 277 n n C3D C4D HEM sing 278 n n C3D CAD HEM sing 279 n n C4D ND HEM sing 280 n n CMD HMD HEM sing 281 n n CMD HMDA HEM sing 282 n n CMD HMDB HEM sing 283 n n CAD CBD HEM sing 284 n n CAD HAD HEM sing 285 n n CAD HADA HEM sing 286 n n CBD CGD HEM sing 287 n n CBD HBD HEM sing 288 n n CBD HBDA HEM sing 289 n n CGD O1D HEM doub 290 n n CGD O2D HEM sing 291 n n O2A H2A HEM sing 292 n n O2D H2D HEM sing 293 n n FE NA HEM sing 294 n n FE NB HEM sing 295 n n FE NC HEM sing 296 n n FE ND HEM sing 297 n n # _atom_sites.entry_id 5JKV _atom_sites.fract_transf_matrix[1][1] 0.007132 _atom_sites.fract_transf_matrix[1][2] 0.004118 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008235 _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] 0.008384 _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 1 601 600 HEM HEM . C 3 ASD A 1 602 601 ASD ASD . D 4 1PE A 1 603 602 1PE P5G . E 5 PO4 A 1 604 60 PO4 PO4 . F 5 PO4 A 1 605 61 PO4 PO4 . G 5 PO4 A 1 606 62 PO4 PO4 . H 5 PO4 A 1 607 63 PO4 PO4 . I 6 HOH A 1 701 7 HOH HOH . I 6 HOH A 2 702 30 HOH HOH . I 6 HOH A 3 703 34 HOH HOH . I 6 HOH A 4 704 41 HOH HOH . I 6 HOH A 5 705 16 HOH HOH . I 6 HOH A 6 706 2 HOH HOH . I 6 HOH A 7 707 39 HOH HOH . I 6 HOH A 8 708 20 HOH HOH . I 6 HOH A 9 709 35 HOH HOH . I 6 HOH A 10 710 21 HOH HOH . I 6 HOH A 11 711 13 HOH HOH . I 6 HOH A 12 712 22 HOH HOH . I 6 HOH A 13 713 19 HOH HOH . I 6 HOH A 14 714 6 HOH HOH . I 6 HOH A 15 715 33 HOH HOH . I 6 HOH A 16 716 3 HOH HOH . I 6 HOH A 17 717 32 HOH HOH . I 6 HOH A 18 718 43 HOH HOH . I 6 HOH A 19 719 40 HOH HOH . I 6 HOH A 20 720 17 HOH HOH . I 6 HOH A 21 721 9 HOH HOH . I 6 HOH A 22 722 18 HOH HOH . I 6 HOH A 23 723 14 HOH HOH . I 6 HOH A 24 724 24 HOH HOH . I 6 HOH A 25 725 42 HOH HOH . I 6 HOH A 26 726 10 HOH HOH . I 6 HOH A 27 727 27 HOH HOH . I 6 HOH A 28 728 5 HOH HOH . I 6 HOH A 29 729 15 HOH HOH . I 6 HOH A 30 730 12 HOH HOH . I 6 HOH A 31 731 23 HOH HOH . I 6 HOH A 32 732 11 HOH HOH . I 6 HOH A 33 733 1 HOH HOH . I 6 HOH A 34 734 26 HOH HOH . I 6 HOH A 35 735 8 HOH HOH . I 6 HOH A 36 736 37 HOH HOH . I 6 HOH A 37 737 31 HOH HOH . I 6 HOH A 38 738 28 HOH HOH . I 6 HOH A 39 739 25 HOH HOH . I 6 HOH A 40 740 38 HOH HOH . I 6 HOH A 41 741 36 HOH HOH . I 6 HOH A 42 742 4 HOH HOH . I 6 HOH A 43 743 29 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 86.334 52.433 41.132 1 45.92 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 81.833 51.017 42.146 1 45.91 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 83.525 46.63 43.201 1 46.36 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 88.012 47.948 42.073 1 45.88 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 84.968 52.422 41.272 1 45.36 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 84.079 53.526 40.955 1 45.97 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 82.833 53.133 41.227 1 45.2 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 82.901 51.773 41.723 1 45.62 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 81.542 53.967 41.052 1 44.41 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 84.502 54.902 40.378 1 46.27 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 84.615 54.749 38.864 1 48.1 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 84.688 56.08 38.153 1 51.53 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 85.457 56.988 38.596 1 53.84 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 83.983 56.243 37.12 1 51.16 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 81.915 49.74 42.63 1 45.53 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 80.857 48.984 43.279 1 46.4 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 81.343 47.769 43.564 1 46.98 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 82.708 47.729 43.099 1 46.78 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 79.435 49.509 43.581 1 44.35 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 80.652 46.574 44.271 1 47.87 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 79.327 46.416 44.255 1 48.55 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 84.866 46.591 42.948 1 45.87 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 85.711 45.42 43.068 1 46.53 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 86.966 45.787 42.753 1 46.86 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 86.93 47.199 42.434 1 46.37 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 85.215 44.017 43.48 1 45.36 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 88.24 44.909 42.711 1 47.31 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 88.453 43.922 43.596 1 48.19 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 87.992 49.289 41.771 1 46.28 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 89.174 50.081 41.497 1 46.68 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 88.66 51.489 41.206 1 47.03 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 87.214 51.393 41.327 1 46.6 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 90.638 49.6 41.509 1 45.31 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 89.517 52.719 40.838 1 48.01 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 89.576 52.763 39.313 1 49.82 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 90.465 53.873 38.793 1 51.8 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 91.146 53.667 37.75 1 51.08 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 90.487 54.976 39.406 1 52.7 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 84.212 51.366 41.714 1 44.58 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 83.025 48.945 42.53 1 45.62 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 85.63 47.656 42.538 1 45.31 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 86.864 50.088 41.658 1 45.54 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 84.905 49.496 42.077 1 47.46 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #