data_5VCD # _model_server_result.job_id 0gsUzsOKGQMJCoklxRLxNQ _model_server_result.datetime_utc '2024-11-08 04:29:24' _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 5vcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VCD # _exptl.entry_id 5VCD _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 5VCD _cell.length_a 76.46 _cell.length_b 99.66 _cell.length_c 132.89 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VCD _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,I,J,K,L,M,N,O 1 1,2 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 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 -76.46 0 0 3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -76.46 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 # 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 A SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 O O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _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 142 n n CHA C4D HEM doub 143 n n CHA HHA HEM sing 144 n n CHB C4A HEM sing 145 n n CHB C1B HEM doub 146 n n CHB HHB HEM sing 147 n n CHC C4B HEM sing 148 n n CHC C1C HEM doub 149 n n CHC HHC HEM sing 150 n n CHD C4C HEM doub 151 n n CHD C1D HEM sing 152 n n CHD HHD HEM sing 153 n n C1A C2A HEM doub 154 n y C1A NA HEM sing 155 n y C2A C3A HEM sing 156 n y C2A CAA HEM sing 157 n n C3A C4A HEM doub 158 n y C3A CMA HEM sing 159 n n C4A NA HEM sing 160 n y CMA HMA HEM sing 161 n n CMA HMAA HEM sing 162 n n CMA HMAB HEM sing 163 n n CAA CBA HEM sing 164 n n CAA HAA HEM sing 165 n n CAA HAAA HEM sing 166 n n CBA CGA HEM sing 167 n n CBA HBA HEM sing 168 n n CBA HBAA HEM sing 169 n n CGA O1A HEM doub 170 n n CGA O2A HEM sing 171 n n C1B C2B HEM sing 172 n n C1B NB HEM sing 173 n n C2B C3B HEM doub 174 n n C2B CMB HEM sing 175 n n C3B C4B HEM sing 176 n n C3B CAB HEM sing 177 n n C4B NB HEM doub 178 n n CMB HMB HEM sing 179 n n CMB HMBA HEM sing 180 n n CMB HMBB HEM sing 181 n n CAB CBB HEM doub 182 n n CAB HAB HEM sing 183 n n CBB HBB HEM sing 184 n n CBB HBBA HEM sing 185 n n C1C C2C HEM sing 186 n y C1C NC HEM sing 187 n y C2C C3C HEM doub 188 n y C2C CMC HEM sing 189 n n C3C C4C HEM sing 190 n y C3C CAC HEM sing 191 n n C4C NC HEM sing 192 n y CMC HMC HEM sing 193 n n CMC HMCA HEM sing 194 n n CMC HMCB HEM sing 195 n n CAC CBC HEM doub 196 n n CAC HAC HEM sing 197 n n CBC HBC HEM sing 198 n n CBC HBCA HEM sing 199 n n C1D C2D HEM sing 200 n n C1D ND HEM doub 201 n n C2D C3D HEM doub 202 n n C2D CMD HEM sing 203 n n C3D C4D HEM sing 204 n n C3D CAD HEM sing 205 n n C4D ND HEM sing 206 n n CMD HMD HEM sing 207 n n CMD HMDA HEM sing 208 n n CMD HMDB HEM sing 209 n n CAD CBD HEM sing 210 n n CAD HAD HEM sing 211 n n CAD HADA HEM sing 212 n n CBD CGD HEM sing 213 n n CBD HBD HEM sing 214 n n CBD HBDA HEM sing 215 n n CGD O1D HEM doub 216 n n CGD O2D HEM sing 217 n n O2A H2A HEM sing 218 n n O2D H2D HEM sing 219 n n FE NA HEM sing 220 n n FE NB HEM sing 221 n n FE NC HEM sing 222 n n FE ND HEM sing 223 n n # _atom_sites.entry_id 5VCD _atom_sites.fract_transf_matrix[1][1] 0.013079 _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] 0.010034 _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] 0.007525 _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 1 601 500 HEM HEM . C 3 GOL A 1 602 600 GOL GOL . D 3 GOL A 1 603 601 GOL GOL . E 3 GOL A 1 604 602 GOL GOL . F 3 GOL A 1 605 603 GOL GOL . G 3 GOL A 1 606 604 GOL GOL . H 3 GOL A 1 607 605 GOL GOL . I 3 GOL A 1 608 606 GOL GOL . J 3 GOL A 1 609 607 GOL GOL . K 3 GOL A 1 610 608 GOL GOL . L 3 GOL A 1 611 609 GOL GOL . M 3 GOL A 1 612 610 GOL GOL . N 3 GOL A 1 613 611 GOL GOL . O 4 HOH A 1 701 103 HOH HOH . O 4 HOH A 2 702 96 HOH HOH . O 4 HOH A 3 703 68 HOH HOH . O 4 HOH A 4 704 11 HOH HOH . O 4 HOH A 5 705 102 HOH HOH . O 4 HOH A 6 706 45 HOH HOH . O 4 HOH A 7 707 32 HOH HOH . O 4 HOH A 8 708 73 HOH HOH . O 4 HOH A 9 709 20 HOH HOH . O 4 HOH A 10 710 50 HOH HOH . O 4 HOH A 11 711 81 HOH HOH . O 4 HOH A 12 712 58 HOH HOH . O 4 HOH A 13 713 92 HOH HOH . O 4 HOH A 14 714 9 HOH HOH . O 4 HOH A 15 715 30 HOH HOH . O 4 HOH A 16 716 95 HOH HOH . O 4 HOH A 17 717 74 HOH HOH . O 4 HOH A 18 718 29 HOH HOH . O 4 HOH A 19 719 17 HOH HOH . O 4 HOH A 20 720 14 HOH HOH . O 4 HOH A 21 721 7 HOH HOH . O 4 HOH A 22 722 72 HOH HOH . O 4 HOH A 23 723 15 HOH HOH . O 4 HOH A 24 724 34 HOH HOH . O 4 HOH A 25 725 36 HOH HOH . O 4 HOH A 26 726 93 HOH HOH . O 4 HOH A 27 727 70 HOH HOH . O 4 HOH A 28 728 5 HOH HOH . O 4 HOH A 29 729 61 HOH HOH . O 4 HOH A 30 730 31 HOH HOH . O 4 HOH A 31 731 22 HOH HOH . O 4 HOH A 32 732 52 HOH HOH . O 4 HOH A 33 733 82 HOH HOH . O 4 HOH A 34 734 27 HOH HOH . O 4 HOH A 35 735 47 HOH HOH . O 4 HOH A 36 736 71 HOH HOH . O 4 HOH A 37 737 39 HOH HOH . O 4 HOH A 38 738 12 HOH HOH . O 4 HOH A 39 739 25 HOH HOH . O 4 HOH A 40 740 19 HOH HOH . O 4 HOH A 41 741 62 HOH HOH . O 4 HOH A 42 742 91 HOH HOH . O 4 HOH A 43 743 10 HOH HOH . O 4 HOH A 44 744 88 HOH HOH . O 4 HOH A 45 745 101 HOH HOH . O 4 HOH A 46 746 106 HOH HOH . O 4 HOH A 47 747 53 HOH HOH . O 4 HOH A 48 748 89 HOH HOH . O 4 HOH A 49 749 46 HOH HOH . O 4 HOH A 50 750 51 HOH HOH . O 4 HOH A 51 751 35 HOH HOH . O 4 HOH A 52 752 42 HOH HOH . O 4 HOH A 53 753 67 HOH HOH . O 4 HOH A 54 754 80 HOH HOH . O 4 HOH A 55 755 78 HOH HOH . O 4 HOH A 56 756 2 HOH HOH . O 4 HOH A 57 757 65 HOH HOH . O 4 HOH A 58 758 86 HOH HOH . O 4 HOH A 59 759 28 HOH HOH . O 4 HOH A 60 760 49 HOH HOH . O 4 HOH A 61 761 38 HOH HOH . O 4 HOH A 62 762 54 HOH HOH . O 4 HOH A 63 763 56 HOH HOH . O 4 HOH A 64 764 33 HOH HOH . O 4 HOH A 65 765 23 HOH HOH . O 4 HOH A 66 766 90 HOH HOH . O 4 HOH A 67 767 4 HOH HOH . O 4 HOH A 68 768 6 HOH HOH . O 4 HOH A 69 769 18 HOH HOH . O 4 HOH A 70 770 24 HOH HOH . O 4 HOH A 71 771 64 HOH HOH . O 4 HOH A 72 772 79 HOH HOH . O 4 HOH A 73 773 13 HOH HOH . O 4 HOH A 74 774 41 HOH HOH . O 4 HOH A 75 775 40 HOH HOH . O 4 HOH A 76 776 3 HOH HOH . O 4 HOH A 77 777 37 HOH HOH . O 4 HOH A 78 778 26 HOH HOH . O 4 HOH A 79 779 98 HOH HOH . O 4 HOH A 80 780 43 HOH HOH . O 4 HOH A 81 781 83 HOH HOH . O 4 HOH A 82 782 44 HOH HOH . O 4 HOH A 83 783 84 HOH HOH . O 4 HOH A 84 784 63 HOH HOH . O 4 HOH A 85 785 85 HOH HOH . O 4 HOH A 86 786 21 HOH HOH . O 4 HOH A 87 787 94 HOH HOH . O 4 HOH A 88 788 75 HOH HOH . O 4 HOH A 89 789 97 HOH HOH . O 4 HOH A 90 790 104 HOH HOH . O 4 HOH A 91 791 76 HOH HOH . O 4 HOH A 92 792 59 HOH HOH . O 4 HOH A 93 793 57 HOH HOH . O 4 HOH A 94 794 55 HOH HOH . O 4 HOH A 95 795 8 HOH HOH . O 4 HOH A 96 796 77 HOH HOH . O 4 HOH A 97 797 87 HOH HOH . O 4 HOH A 98 798 60 HOH HOH . O 4 HOH A 99 799 99 HOH HOH . O 4 HOH A 100 800 16 HOH HOH . O 4 HOH A 101 801 48 HOH HOH . O 4 HOH A 102 802 100 HOH HOH . O 4 HOH A 103 803 69 HOH HOH . O 4 HOH A 104 804 1 HOH HOH . O 4 HOH A 105 805 66 HOH HOH . O 4 HOH A 106 806 105 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 -15.181 -19.722 -10.746 1 41.04 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . B 2 -15.962 -22.413 -14.697 1 38.35 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . B 2 -16.405 -26.358 -11.933 1 42.64 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . B 2 -15.365 -23.765 -8.015 1 41.32 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . B 2 -15.336 -20.106 -12.042 1 39.42 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . B 2 -15.249 -19.225 -13.183 1 40.59 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . B 2 -15.457 -19.963 -14.283 1 43.89 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . B 2 -15.693 -21.338 -13.869 1 41.52 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . B 2 -15.447 -19.46 -15.743 1 39.36 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . B 2 -14.945 -17.711 -13.113 1 36.59 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . B 2 -13.43 -17.543 -13.306 1 40.19 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . B 2 -13.052 -16.087 -13.474 1 36.82 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . B 2 -11.931 -15.795 -13.985 1 38.35 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . B 2 -13.876 -15.226 -13.087 1 39.88 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . B 2 -16.17 -23.719 -14.298 1 38.26 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . B 2 -16.49 -24.84 -15.175 1 37.39 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . B 2 -16.633 -25.933 -14.406 1 44.39 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . B 2 -16.386 -25.532 -13.029 1 43.13 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . B 2 -16.644 -24.701 -16.706 1 38.04 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . B 2 -16.954 -27.386 -14.818 1 46.1 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . B 2 -16.503 -27.933 -15.952 1 47.98 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . B 2 -16.064 -26.033 -10.64 1 43.97 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . B 2 -15.865 -26.959 -9.534 1 40.7 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . B 2 -15.567 -26.266 -8.442 1 40.62 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . B 2 -15.588 -24.85 -8.819 1 39.85 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . B 2 -15.963 -28.5 -9.616 1 39.83 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . B 2 -15.288 -26.946 -7.066 1 40.62 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . B 2 -14.768 -26.267 -6.049 1 50.4 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . B 2 -15.275 -22.442 -8.368 1 42.94 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . B 2 -15.077 -21.353 -7.43 1 39.5 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . B 2 -15.026 -20.096 -8.288 1 42.84 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . B 2 -15.176 -20.546 -9.654 1 45.25 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . B 2 -14.961 -21.403 -5.901 1 41.64 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . B 2 -14.81 -18.668 -7.777 1 39.54 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . B 2 -13.314 -18.548 -7.498 1 37.53 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . B 2 -13.013 -17.223 -6.826 1 38.41 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . B 2 -11.943 -17.111 -6.174 1 46.99 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . B 2 -13.847 -16.299 -6.937 1 44.16 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . B 2 -15.614 -21.377 -12.493 1 39.6 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . B 2 -16.12 -24.189 -13.01 1 37.14 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . B 2 -15.892 -24.763 -10.162 1 35.61 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . B 2 -15.334 -21.915 -9.656 1 39.44 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . B 2 -15.622 -23.071 -11.352 1 39.9 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #