data_3VU3 # _model_server_result.job_id 1I1Uo2niv1EU_fLz2ECH9g _model_server_result.datetime_utc '2024-11-12 23:05:29' _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 3vu3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":801}' # _entry.id 3VU3 # _exptl.entry_id 3VU3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 3VU3 _cell.length_a 136.432 _cell.length_b 159.009 _cell.length_c 167.181 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VU3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 28-meric _pdbx_struct_assembly.oligomeric_count 28 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 136.432 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 136.432 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 3 _struct_asym.id H _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 covale ? covale1 A ND1 HIS 392 A HIS 392 1_555 A CB TYR 415 A TYR 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.695 ? metalc ? metalc1 A OH TYR 415 A TYR 415 1_555 H FE HEM . A HEM 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 3VU3 _atom_sites.fract_transf_matrix[1][1] 0.00733 _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] 0.006289 _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] 0.005982 _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 H 3 HEM A 1 801 754 HEM HEM . I 4 HOH A 1 901 1 HOH HOH . I 4 HOH A 2 902 3 HOH HOH . I 4 HOH A 3 903 4 HOH HOH . I 4 HOH A 4 904 5 HOH HOH . I 4 HOH A 5 905 6 HOH HOH . I 4 HOH A 6 906 7 HOH HOH . I 4 HOH A 7 907 8 HOH HOH . I 4 HOH A 8 908 9 HOH HOH . I 4 HOH A 9 909 10 HOH HOH . I 4 HOH A 10 910 12 HOH HOH . I 4 HOH A 11 911 13 HOH HOH . I 4 HOH A 12 912 14 HOH HOH . I 4 HOH A 13 913 15 HOH HOH . I 4 HOH A 14 914 16 HOH HOH . I 4 HOH A 15 915 17 HOH HOH . I 4 HOH A 16 916 18 HOH HOH . I 4 HOH A 17 917 19 HOH HOH . I 4 HOH A 18 918 20 HOH HOH . I 4 HOH A 19 919 22 HOH HOH . I 4 HOH A 20 920 23 HOH HOH . I 4 HOH A 21 921 24 HOH HOH . I 4 HOH A 22 922 25 HOH HOH . I 4 HOH A 23 923 26 HOH HOH . I 4 HOH A 24 924 27 HOH HOH . I 4 HOH A 25 925 28 HOH HOH . I 4 HOH A 26 926 29 HOH HOH . J 4 HOH D 1 201 21 HOH HOH . K 4 HOH G 1 201 11 HOH HOH . L 4 HOH H 1 201 2 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 . . . H 3 63.607 13.648 14.485 1 20.23 ? CHA HEM 801 A 1 HETATM 2 C CHB HEM . . . H 3 62.224 17.585 17.117 1 19.29 ? CHB HEM 801 A 1 HETATM 3 C CHC HEM . . . H 3 66.24 19.782 15.684 1 19.34 ? CHC HEM 801 A 1 HETATM 4 C CHD HEM . . . H 3 66.633 16.408 12.019 1 19.49 ? CHD HEM 801 A 1 HETATM 5 C C1A HEM . . . H 3 62.994 14.551 15.436 1 19.37 ? C1A HEM 801 A 1 HETATM 6 C C2A HEM . . . H 3 61.98 14.034 16.388 1 18.42 ? C2A HEM 801 A 1 HETATM 7 C C3A HEM . . . H 3 61.578 15.198 17.131 1 17.92 ? C3A HEM 801 A 1 HETATM 8 C C4A HEM . . . H 3 62.424 16.265 16.6 1 18.11 ? C4A HEM 801 A 1 HETATM 9 C CMA HEM . . . H 3 60.561 15.289 18.234 1 19.1 ? CMA HEM 801 A 1 HETATM 10 C CAA HEM . . . H 3 61.421 12.653 16.524 1 19 ? CAA HEM 801 A 1 HETATM 11 C CBA HEM . . . H 3 60.361 12.58 15.408 1 20.39 ? CBA HEM 801 A 1 HETATM 12 C CGA HEM . . . H 3 59.489 11.331 15.43 1 20.75 ? CGA HEM 801 A 1 HETATM 13 O O1A HEM . . . H 3 59.416 10.722 14.311 1 22.36 ? O1A HEM 801 A 1 HETATM 14 O O2A HEM . . . H 3 58.899 10.998 16.505 1 18.75 ? O2A HEM 801 A 1 HETATM 15 C C1B HEM . . . H 3 63.258 18.566 16.993 1 19.77 ? C1B HEM 801 A 1 HETATM 16 C C2B HEM . . . H 3 63.074 19.87 17.676 1 20.21 ? C2B HEM 801 A 1 HETATM 17 C C3B HEM . . . H 3 64.305 20.469 17.233 1 21.13 ? C3B HEM 801 A 1 HETATM 18 C C4B HEM . . . H 3 64.986 19.485 16.352 1 20.24 ? C4B HEM 801 A 1 HETATM 19 C CMB HEM . . . H 3 61.995 20.397 18.583 1 19.21 ? CMB HEM 801 A 1 HETATM 20 C CAB HEM . . . H 3 64.769 21.805 17.599 1 23.01 ? CAB HEM 801 A 1 HETATM 21 C CBB HEM . . . H 3 64.279 22.792 16.876 1 25.96 ? CBB HEM 801 A 1 HETATM 22 C C1C HEM . . . H 3 66.681 19.107 14.486 1 19.46 ? C1C HEM 801 A 1 HETATM 23 C C2C HEM . . . H 3 67.794 19.596 13.607 1 19.14 ? C2C HEM 801 A 1 HETATM 24 C C3C HEM . . . H 3 67.851 18.557 12.558 1 19.39 ? C3C HEM 801 A 1 HETATM 25 C C4C HEM . . . H 3 66.844 17.547 12.856 1 19.04 ? C4C HEM 801 A 1 HETATM 26 C CMC HEM . . . H 3 68.645 20.825 13.741 1 17.91 ? CMC HEM 801 A 1 HETATM 27 C CAC HEM . . . H 3 68.782 18.51 11.418 1 20.58 ? CAC HEM 801 A 1 HETATM 28 C CBC HEM . . . H 3 69.307 19.683 11.078 1 22.8 ? CBC HEM 801 A 1 HETATM 29 C C1D HEM . . . H 3 65.84 15.269 12.436 1 20.45 ? C1D HEM 801 A 1 HETATM 30 C C2D HEM . . . H 3 65.756 14.054 11.574 1 21.14 ? C2D HEM 801 A 1 HETATM 31 C C3D HEM . . . H 3 64.796 13.224 12.331 1 20.63 ? C3D HEM 801 A 1 HETATM 32 C C4D HEM . . . H 3 64.511 14.103 13.471 1 20.24 ? C4D HEM 801 A 1 HETATM 33 C CMD HEM . . . H 3 66.495 13.861 10.286 1 20.39 ? CMD HEM 801 A 1 HETATM 34 C CAD HEM . . . H 3 64.197 11.875 12.284 1 20.88 ? CAD HEM 801 A 1 HETATM 35 C CBD HEM . . . H 3 64.265 11.129 11.022 1 25.32 ? CBD HEM 801 A 1 HETATM 36 C CGD HEM . . . H 3 62.838 11.293 10.513 1 29.96 ? CGD HEM 801 A 1 HETATM 37 O O1D HEM . . . H 3 62.608 11.368 9.288 1 27.87 ? O1D HEM 801 A 1 HETATM 38 O O2D HEM . . . H 3 61.876 11.331 11.327 1 37.68 ? O2D HEM 801 A 1 HETATM 39 N NA HEM . . . H 3 63.22 15.991 15.413 1 18.76 ? NA HEM 801 A 1 HETATM 40 N NB HEM . . . H 3 64.324 18.356 16.185 1 19.12 ? NB HEM 801 A 1 HETATM 41 N NC HEM . . . H 3 65.987 17.945 13.951 1 19.53 ? NC HEM 801 A 1 HETATM 42 N ND HEM . . . H 3 65.071 15.301 13.537 1 19.5 ? ND HEM 801 A 1 HETATM 43 FE FE HEM . . . H 3 64.963 16.742 15.034 1 19.26 ? FE HEM 801 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #