data_5BV5 # _model_server_result.job_id bjc0JOd8iGCI_RMFc9bTaw _model_server_result.datetime_utc '2024-11-01 13:31:15' _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 5bv5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":500}' # _entry.id 5BV5 # _exptl.entry_id 5BV5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.18 _cell.angle_gamma 90 _cell.entry_id 5BV5 _cell.length_a 64.486 _cell.length_b 137.871 _cell.length_c 91.779 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BV5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA tetrameric 4 software_defined_assembly 5 PISA tetrameric 4 software_defined_assembly 6 PISA dimeric 2 software_defined_assembly 7 PISA dimeric 2 software_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,N 1 1 B,G,H,I,O 2 1 C,J,K,P 3 1 D,L,M,Q 4 1 B,C,G,H,I,J,K,O,P 5 1 A,D,E,F,L,M,N,Q 5 2 B,G,H,I,O 6 1 D,L,M,Q 6 2 A,E,F,N 6 4 C,J,K,P 6 5 A,E,F,N 7 1 C,J,K,P 7 3 B,G,H,I,O 8 1 D,L,M,Q 8 2 # 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' 1_454 x-1,y,z-1 1 0 0 0 1 0 0 0 1 -46.690793 0 -90.0373 3 'crystal symmetry operation' 1_656 x+1,y,z+1 1 0 0 0 1 0 0 0 1 46.690793 0 90.0373 4 'crystal symmetry operation' 2_444 -x-1,y-1/2,-z-1 -1 0 0 0 1 0 0 0 -1 -46.690793 -68.9355 -90.0373 5 'crystal symmetry operation' 2_343 -x-2,y-1/2,-z-2 -1 0 0 0 1 0 0 0 -1 -93.381587 -68.9355 -180.074601 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 metalc ? metalc1 A NE2 HIS 317 A HIS 317 1_555 F FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? metalc ? metalc2 F FE HEM . A HEM 602 1_555 N O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc3 B NE2 HIS 317 B HIS 317 1_555 H FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc4 H FE HEM . B HEM 602 1_555 I N3 PIM . B PIM 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc5 C NE2 HIS 317 D HIS 317 1_555 J FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? metalc ? metalc6 J FE HEM . D HEM 500 1_555 K N3 PIM . D PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc7 D NE2 HIS 317 C HIS 317 1_555 L FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc8 L FE HEM . C HEM 500 1_555 M N3 PIM . C PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 5BV5 _atom_sites.fract_transf_matrix[1][1] 0.015507 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003064 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007253 _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] 0.011106 _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 E 2 PO4 A 1 601 2 PO4 PO4 . F 3 HEM A 1 602 500 HEM HEM . G 2 PO4 B 1 601 1 PO4 PO4 . H 3 HEM B 1 602 500 HEM HEM . I 4 PIM B 1 603 501 PIM PIM . J 3 HEM D 1 500 500 HEM HEM . K 4 PIM D 1 501 501 PIM PIM . L 3 HEM C 1 500 500 HEM HEM . M 4 PIM C 1 501 501 PIM PIM . N 5 HOH A 1 701 9 HOH HOH . N 5 HOH A 2 702 1 HOH HOH . O 5 HOH B 1 701 4 HOH HOH . O 5 HOH B 2 702 11 HOH HOH . O 5 HOH B 3 703 5 HOH HOH . P 5 HOH D 1 601 10 HOH HOH . P 5 HOH D 2 602 7 HOH HOH . P 5 HOH D 3 603 2 HOH HOH . Q 5 HOH C 1 601 3 HOH HOH . Q 5 HOH C 2 602 8 HOH HOH . Q 5 HOH C 3 603 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 . . . J 3 -51.543 -2.02 -50.993 1 55.43 ? CHA HEM 500 D 1 HETATM 2 C CHB HEM . . . J 3 -52.788 -4.912 -47.319 1 52.36 ? CHB HEM 500 D 1 HETATM 3 C CHC HEM . . . J 3 -57.226 -5.454 -49.277 1 50.39 ? CHC HEM 500 D 1 HETATM 4 C CHD HEM . . . J 3 -55.899 -2.677 -53.006 1 52.31 ? CHD HEM 500 D 1 HETATM 5 C C1A HEM . . . J 3 -51.518 -2.737 -49.827 1 54.84 ? C1A HEM 500 D 1 HETATM 6 C C2A HEM . . . J 3 -50.423 -2.775 -48.945 1 55.53 ? C2A HEM 500 D 1 HETATM 7 C C3A HEM . . . J 3 -50.767 -3.583 -47.908 1 55.26 ? C3A HEM 500 D 1 HETATM 8 C C4A HEM . . . J 3 -52.076 -4.064 -48.156 1 54.02 ? C4A HEM 500 D 1 HETATM 9 C CMA HEM . . . J 3 -49.893 -3.904 -46.72 1 55.44 ? CMA HEM 500 D 1 HETATM 10 C CAA HEM . . . J 3 -49.129 -2.023 -49.123 1 57.3 ? CAA HEM 500 D 1 HETATM 11 C CBA HEM . . . J 3 -49.388 -0.546 -48.803 1 59.4 ? CBA HEM 500 D 1 HETATM 12 C CGA HEM . . . J 3 -48.094 0.194 -48.579 1 60.58 ? CGA HEM 500 D 1 HETATM 13 O O1A HEM . . . J 3 -47.067 -0.119 -49.224 1 61.61 ? O1A HEM 500 D 1 HETATM 14 O O2A HEM . . . J 3 -48.05 1.13 -47.748 1 60.65 ? O2A HEM 500 D 1 HETATM 15 C C1B HEM . . . J 3 -54.122 -5.305 -47.536 1 50.89 ? C1B HEM 500 D 1 HETATM 16 C C2B HEM . . . J 3 -54.842 -6.167 -46.656 1 49.21 ? C2B HEM 500 D 1 HETATM 17 C C3B HEM . . . J 3 -56.098 -6.335 -47.184 1 48.77 ? C3B HEM 500 D 1 HETATM 18 C C4B HEM . . . J 3 -56.115 -5.529 -48.429 1 50.11 ? C4B HEM 500 D 1 HETATM 19 C CMB HEM . . . J 3 -54.305 -6.769 -45.38 1 48.67 ? CMB HEM 500 D 1 HETATM 20 C CAB HEM . . . J 3 -57.259 -7.116 -46.692 1 48.08 ? CAB HEM 500 D 1 HETATM 21 C CBB HEM . . . J 3 -57.281 -7.811 -45.557 1 47.98 ? CBB HEM 500 D 1 HETATM 22 C C1C HEM . . . J 3 -57.262 -4.745 -50.476 1 50.57 ? C1C HEM 500 D 1 HETATM 23 C C2C HEM . . . J 3 -58.391 -4.601 -51.302 1 50.94 ? C2C HEM 500 D 1 HETATM 24 C C3C HEM . . . J 3 -58.017 -3.803 -52.378 1 51.14 ? C3C HEM 500 D 1 HETATM 25 C C4C HEM . . . J 3 -56.646 -3.469 -52.177 1 51.54 ? C4C HEM 500 D 1 HETATM 26 C CMC HEM . . . J 3 -59.747 -5.218 -51.042 1 51.28 ? CMC HEM 500 D 1 HETATM 27 C CAC HEM . . . J 3 -58.817 -3.339 -53.535 1 50.42 ? CAC HEM 500 D 1 HETATM 28 C CBC HEM . . . J 3 -60.106 -3.608 -53.719 1 50.95 ? CBC HEM 500 D 1 HETATM 29 C C1D HEM . . . J 3 -54.596 -2.304 -52.688 1 53.61 ? C1D HEM 500 D 1 HETATM 30 C C2D HEM . . . J 3 -53.852 -1.438 -53.614 1 55.43 ? C2D HEM 500 D 1 HETATM 31 C C3D HEM . . . J 3 -52.647 -1.255 -53.055 1 58.38 ? C3D HEM 500 D 1 HETATM 32 C C4D HEM . . . J 3 -52.671 -2.012 -51.798 1 55.43 ? C4D HEM 500 D 1 HETATM 33 C CMD HEM . . . J 3 -54.332 -0.864 -54.925 1 55.24 ? CMD HEM 500 D 1 HETATM 34 C CAD HEM . . . J 3 -51.494 -0.449 -53.605 1 63.77 ? CAD HEM 500 D 1 HETATM 35 C CBD HEM . . . J 3 -51.293 0.844 -52.802 1 68.34 ? CBD HEM 500 D 1 HETATM 36 C CGD HEM . . . J 3 -49.889 1.366 -53.019 1 73.12 ? CGD HEM 500 D 1 HETATM 37 O O1D HEM . . . J 3 -49.254 1.884 -52.069 1 76.94 ? O1D HEM 500 D 1 HETATM 38 O O2D HEM . . . J 3 -49.351 1.285 -54.148 1 76.69 ? O2D HEM 500 D 1 HETATM 39 N NA HEM . . . J 3 -52.513 -3.554 -49.356 1 53.43 ? NA HEM 500 D 1 HETATM 40 N NB HEM . . . J 3 -54.91 -4.963 -48.559 1 50.93 ? NB HEM 500 D 1 HETATM 41 N NC HEM . . . J 3 -56.203 -4.066 -51.031 1 50.99 ? NC HEM 500 D 1 HETATM 42 N ND HEM . . . J 3 -53.852 -2.633 -51.614 1 54.26 ? ND HEM 500 D 1 HETATM 43 FE FE HEM . . . J 3 -54.341 -3.694 -50.13 1 51.96 ? FE HEM 500 D 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #