data_5VCG # _model_server_result.job_id ffC1gN_TUEKmMh-jXJC8sg _model_server_result.datetime_utc '2024-11-08 04:42:45' _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 5vcg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VCG # _exptl.entry_id 5VCG _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 90 _cell.entry_id 5VCG _cell.length_a 76.539 _cell.length_b 100.459 _cell.length_c 133.679 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VCG _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,E,F,G,H 1 1,2 A,B,C,D,E,F,G,H 2 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -77.34 0 0 3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -77.34 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 422 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 442 _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 2.3 _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 231 n n CHA C4D HEM doub 232 n n CHA HHA HEM sing 233 n n CHB C4A HEM sing 234 n n CHB C1B HEM doub 235 n n CHB HHB HEM sing 236 n n CHC C4B HEM sing 237 n n CHC C1C HEM doub 238 n n CHC HHC HEM sing 239 n n CHD C4C HEM doub 240 n n CHD C1D HEM sing 241 n n CHD HHD HEM sing 242 n n C1A C2A HEM doub 243 n y C1A NA HEM sing 244 n y C2A C3A HEM sing 245 n y C2A CAA HEM sing 246 n n C3A C4A HEM doub 247 n y C3A CMA HEM sing 248 n n C4A NA HEM sing 249 n y CMA HMA HEM sing 250 n n CMA HMAA HEM sing 251 n n CMA HMAB HEM sing 252 n n CAA CBA HEM sing 253 n n CAA HAA HEM sing 254 n n CAA HAAA HEM sing 255 n n CBA CGA HEM sing 256 n n CBA HBA HEM sing 257 n n CBA HBAA HEM sing 258 n n CGA O1A HEM doub 259 n n CGA O2A HEM sing 260 n n C1B C2B HEM sing 261 n n C1B NB HEM sing 262 n n C2B C3B HEM doub 263 n n C2B CMB HEM sing 264 n n C3B C4B HEM sing 265 n n C3B CAB HEM sing 266 n n C4B NB HEM doub 267 n n CMB HMB HEM sing 268 n n CMB HMBA HEM sing 269 n n CMB HMBB HEM sing 270 n n CAB CBB HEM doub 271 n n CAB HAB HEM sing 272 n n CBB HBB HEM sing 273 n n CBB HBBA HEM sing 274 n n C1C C2C HEM sing 275 n y C1C NC HEM sing 276 n y C2C C3C HEM doub 277 n y C2C CMC HEM sing 278 n n C3C C4C HEM sing 279 n y C3C CAC HEM sing 280 n n C4C NC HEM sing 281 n y CMC HMC HEM sing 282 n n CMC HMCA HEM sing 283 n n CMC HMCB HEM sing 284 n n CAC CBC HEM doub 285 n n CAC HAC HEM sing 286 n n CBC HBC HEM sing 287 n n CBC HBCA HEM sing 288 n n C1D C2D HEM sing 289 n n C1D ND HEM doub 290 n n C2D C3D HEM doub 291 n n C2D CMD HEM sing 292 n n C3D C4D HEM sing 293 n n C3D CAD HEM sing 294 n n C4D ND HEM sing 295 n n CMD HMD HEM sing 296 n n CMD HMDA HEM sing 297 n n CMD HMDB HEM sing 298 n n CAD CBD HEM sing 299 n n CAD HAD HEM sing 300 n n CAD HADA HEM sing 301 n n CBD CGD HEM sing 302 n n CBD HBD HEM sing 303 n n CBD HBDA HEM sing 304 n n CGD O1D HEM doub 305 n n CGD O2D HEM sing 306 n n O2A H2A HEM sing 307 n n O2D H2D HEM sing 308 n n FE NA HEM sing 309 n n FE NB HEM sing 310 n n FE NC HEM sing 311 n n FE ND HEM sing 312 n n # _atom_sites.entry_id 5VCG _atom_sites.fract_transf_matrix[1][1] 0.013065 _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] 0.009954 _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] 0.007481 _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 1 601 599 HEM HEM . C 3 08Y A 1 602 600 08Y 08Y . D 4 GOL A 1 603 700 GOL GOL . E 4 GOL A 1 604 701 GOL GOL . F 4 GOL A 1 605 702 GOL GOL . G 4 GOL A 1 606 703 GOL GOL . H 5 HOH A 1 701 4 HOH HOH . H 5 HOH A 2 702 33 HOH HOH . H 5 HOH A 3 703 76 HOH HOH . H 5 HOH A 4 704 49 HOH HOH . H 5 HOH A 5 705 55 HOH HOH . H 5 HOH A 6 706 57 HOH HOH . H 5 HOH A 7 707 52 HOH HOH . H 5 HOH A 8 708 28 HOH HOH . H 5 HOH A 9 709 46 HOH HOH . H 5 HOH A 10 710 45 HOH HOH . H 5 HOH A 11 711 6 HOH HOH . H 5 HOH A 12 712 10 HOH HOH . H 5 HOH A 13 713 51 HOH HOH . H 5 HOH A 14 714 14 HOH HOH . H 5 HOH A 15 715 1 HOH HOH . H 5 HOH A 16 716 60 HOH HOH . H 5 HOH A 17 717 38 HOH HOH . H 5 HOH A 18 718 53 HOH HOH . H 5 HOH A 19 719 30 HOH HOH . H 5 HOH A 20 720 20 HOH HOH . H 5 HOH A 21 721 19 HOH HOH . H 5 HOH A 22 722 21 HOH HOH . H 5 HOH A 23 723 65 HOH HOH . H 5 HOH A 24 724 11 HOH HOH . H 5 HOH A 25 725 68 HOH HOH . H 5 HOH A 26 726 42 HOH HOH . H 5 HOH A 27 727 17 HOH HOH . H 5 HOH A 28 728 61 HOH HOH . H 5 HOH A 29 729 5 HOH HOH . H 5 HOH A 30 730 22 HOH HOH . H 5 HOH A 31 731 16 HOH HOH . H 5 HOH A 32 732 47 HOH HOH . H 5 HOH A 33 733 67 HOH HOH . H 5 HOH A 34 734 66 HOH HOH . H 5 HOH A 35 735 39 HOH HOH . H 5 HOH A 36 736 31 HOH HOH . H 5 HOH A 37 737 71 HOH HOH . H 5 HOH A 38 738 54 HOH HOH . H 5 HOH A 39 739 15 HOH HOH . H 5 HOH A 40 740 29 HOH HOH . H 5 HOH A 41 741 2 HOH HOH . H 5 HOH A 42 742 69 HOH HOH . H 5 HOH A 43 743 73 HOH HOH . H 5 HOH A 44 744 36 HOH HOH . H 5 HOH A 45 745 64 HOH HOH . H 5 HOH A 46 746 9 HOH HOH . H 5 HOH A 47 747 40 HOH HOH . H 5 HOH A 48 748 32 HOH HOH . H 5 HOH A 49 749 13 HOH HOH . H 5 HOH A 50 750 62 HOH HOH . H 5 HOH A 51 751 72 HOH HOH . H 5 HOH A 52 752 75 HOH HOH . H 5 HOH A 53 753 34 HOH HOH . H 5 HOH A 54 754 70 HOH HOH . H 5 HOH A 55 755 25 HOH HOH . H 5 HOH A 56 756 56 HOH HOH . H 5 HOH A 57 757 18 HOH HOH . H 5 HOH A 58 758 63 HOH HOH . H 5 HOH A 59 759 37 HOH HOH . H 5 HOH A 60 760 43 HOH HOH . H 5 HOH A 61 761 44 HOH HOH . H 5 HOH A 62 762 24 HOH HOH . H 5 HOH A 63 763 23 HOH HOH . H 5 HOH A 64 764 48 HOH HOH . H 5 HOH A 65 765 27 HOH HOH . H 5 HOH A 66 766 74 HOH HOH . H 5 HOH A 67 767 59 HOH HOH . H 5 HOH A 68 768 26 HOH HOH . H 5 HOH A 69 769 12 HOH HOH . H 5 HOH A 70 770 58 HOH HOH . H 5 HOH A 71 771 41 HOH HOH . H 5 HOH A 72 772 35 HOH HOH . H 5 HOH A 73 773 50 HOH HOH . H 5 HOH A 74 774 7 HOH HOH . H 5 HOH A 75 775 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 . . . B 2 -14.718 -20.088 -10.787 1 53.79 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -15.576 -22.814 -14.681 1 53.06 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -16.046 -26.749 -11.827 1 58.88 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -15.316 -23.962 -7.917 1 52.99 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -14.913 -20.474 -12.089 1 51.68 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -14.936 -19.634 -13.231 1 52.82 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -15.178 -20.412 -14.314 1 51.98 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -15.302 -21.727 -13.854 1 52.9 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -15.265 -19.957 -15.752 1 51.5 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -14.737 -18.133 -13.281 1 48.41 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -13.329 -17.76 -12.865 1 49.7 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -13.073 -16.35 -13.292 1 48.96 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -12.131 -16.141 -14.074 1 49.18 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -13.773 -15.392 -12.875 1 50.57 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -15.803 -24.128 -14.233 1 57.05 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -16.113 -25.177 -15.132 1 59.2 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -16.263 -26.326 -14.372 1 59.86 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -16.031 -25.911 -12.952 1 58.41 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -16.232 -24.975 -16.626 1 57.77 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -16.597 -27.709 -14.807 1 57.68 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -16.589 -28.108 -16.077 1 53.38 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -15.821 -26.341 -10.494 1 58.68 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -15.758 -27.212 -9.367 1 58.15 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -15.546 -26.403 -8.249 1 57.23 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -15.488 -25.053 -8.719 1 54.48 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -15.888 -28.723 -9.393 1 50.52 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -15.41 -26.771 -6.811 1 54.75 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -14.893 -27.903 -6.377 1 54.1 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -15.119 -22.694 -8.448 1 55.28 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -14.892 -21.558 -7.546 1 56.68 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -14.716 -20.491 -8.337 1 57.46 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -14.841 -20.988 -9.722 1 53.66 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -14.866 -21.593 -6.04 1 52.39 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -14.463 -19.066 -7.892 1 56.05 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -13.01 -18.84 -7.491 1 56.5 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -12.832 -17.486 -6.831 1 57.75 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -11.97 -17.307 -5.939 1 56.21 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -13.523 -16.513 -7.188 1 57.87 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -15.172 -21.742 -12.479 1 53.98 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -15.739 -24.612 -12.975 1 59.27 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -15.639 -25.038 -10.065 1 54.01 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -15.047 -22.329 -9.742 1 52.54 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -15.33 -23.376 -11.326 1 51.71 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 43 #